+++ /dev/null
-# Adding stuff to the wiki, like images and documents
-svn co https://biopieces.googlecode.com/svn/wiki wiki --username martinahansen
+++ /dev/null
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
-\begin_document
-\begin_header
-\textclass scrartcl
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-\usepackage[colorlinks=true, urlcolor=blue, linkcolor=black]{hyperref}
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-\author ""
-\author ""
-\end_header
-
-\begin_body
-
-\begin_layout Title
-Biopieces Cookbook
-\end_layout
-
-\begin_layout Author
-Martin Asser Hansen
-\end_layout
-
-\begin_layout Publishers
-John Mattick Group
-\newline
-Institute for Molecular Bioscience
-\newline
-University of Queensland
-\newline
-Aust
-ralia
-\newline
-E-mail: mail@maasha.dk
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
-
-\backslash
-thispagestyle{empty}
-\end_layout
-
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-
-
-\end_layout
-
-\begin_layout Standard
-
-\newpage
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset LatexCommand tableofcontents
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset FloatList figure
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-
-\newpage
-
-\end_layout
-
-\begin_layout Section
-Introduction
-\end_layout
-
-\begin_layout Standard
-Biopieces is a collection of bioinformatic tools that can be linked together
- (piped as we shall call it) in a very flexible manner to perform both simple
- and complex tasks.
- The fundamental idea is that biopieces work on a data stream that will
- only terminate at the end of an analysis and that this data stream can
- be passed through several different biopieces, each performing one specific
- task.
- The advantage of this approach is that a user can perform simple and complex
- tasks without having to write advanced code.
- Moreover, since the data format used to pass data between biopieces is
- text based, biopieces can be written by different developers in their favorite
- programming language --- and still the biopieces will be able to work together.
-\end_layout
-
-\begin_layout Standard
-In the most simple form bioools can be piped together on the command line
- like this (using the pipe character '|'):
-\end_layout
-
-\begin_layout LyX-Code
-read_data | calculate_something | write_result
-\end_layout
-
-\begin_layout Standard
-However, a more comprehensive analysis could be composed:
-\end_layout
-
-\begin_layout LyX-Code
-read_data | select_entries | convert_entries | search_database
-\end_layout
-
-\begin_layout LyX-Code
-evaluate_results | plot_diagram | plot_another_diagram |
-\end_layout
-
-\begin_layout LyX-Code
-load_to_database
-\end_layout
-
-\begin_layout Standard
-The data stream that is piped through the biopieces consists of records
- of key/value pairs in the same way a hash does in order to keep as simple
- a structure as possible.
- An example record can be seen below:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-REC_TYPE: PATSCAN
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-MATCH: AGATCAAGTG
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-S_BEG: 7
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-S_END: 16
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-ALIGN_LEN: 9
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-S_ID: piR-t6
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-STRAND: +
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-PATTERN: AGATCAAGTG
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
----
-\end_layout
-
-\begin_layout Standard
-The '
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-' denotes the delimiter of the records, and each key is a word followed
- by a ':' and a white-space and then the value.
- By convention the biopieces only uses upper case keys (a list of used keys
- can be seen in Appendix\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sec:Keys"
-
-\end_inset
-
-).
- Since the records basically are hash structures this mean that the order
- of the keys in the stream is unordered, and in the above example it is
- pure coincidence that HIT_BEG is displayed before HIT_END, however, when
- the order of the keys is importent, the biopieces will automagically see
- to that.
-\end_layout
-
-\begin_layout Standard
-All of the biopieces are able to read and write a data stream to and from
- file as long as the records are in the biopieces format.
- This means that if you are undertaking a lengthy analysis where one of
- the steps is time consuming, you may save the stream after this step, and
- subsequently start one or more analysis from that last step
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-It is a goal that the biopieces at some point will be able to dump the data
- stream to file in case one of the tools fail critically.
-\end_layout
-
-\end_inset
-
-.
- If you are running a lengthy analysis it is highly recommended that you
- create a small test sample of the data and run that through the pipeline
- --- and once you are satisfied with the result proceed with the full data
- set (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-select-a-few-records"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Standard
-All of the biopieces can be supplied with long arguments prefixed with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
- switches or single character arguments prefixed with - switches that can
- be grouped together (e.g.
- -xok).
- In this cookbook only the long switches are used to emphasize what these
- switches do.
-\end_layout
-
-\begin_layout Section
-Setup
-\end_layout
-
-\begin_layout Standard
-In order to get the biopieces to work, you need to add environment settings
- to include the code binaries, scripts, and modules that constitute the
- biopieces package.
- Assuming that you are using bash, add the following to your '~/.bashrc'
- file using your favorite editor.
- After the changes has been saved you need to either run 'source ~/.bashrc'
- or relogin.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-if [ -f "/home/m.hansen/maasha/conf/bashrc" ]; then
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- source "/home/m.hansen/maasha/conf/bashrc"
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-fi
-\end_layout
-
-\begin_layout Section
-Getting Started
-\end_layout
-
-\begin_layout Standard
-The biopiece
-\series bold
-list_biopieces
-\series default
- lists all the biopieces along with a description:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-list_biopieces
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-align_seq Align sequences in stream using Muscle.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-analyze_seq Analysis the residue composition of each sequence
- in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-analyze_vals Determine type, count, min, max, sum and mean for
- values in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-blast_seq BLAST sequences in stream against a specified database.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-blat_seq BLAT sequences in stream against a specified genome.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-complement_seq Complement sequences in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_records Count the number of records in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_seq Count sequences in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_vals Count the number of times values of given keys exists
- in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-create_blast_db Create a BLAST database from sequences in stream for
- use with BLAST.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-...
-\end_layout
-
-\begin_layout Standard
-To list the biopieces for writing different formats, you can use unix's
- grep like this:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-list_biopieces | grep write
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_align Write aligned sequences in pretty alignment format.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_bed Write records from stream as BED lines.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_blast Write BLAST records from stream in BLAST tabular format
- (-m8 and 9).
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_fasta Write sequences in FASTA format.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_psl Write records from stream in PSL format.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_tab Write records from stream as tab separated table.
-\end_layout
-
-\begin_layout Standard
-In order to find out how a specific biopiece works, you just type the program
- name without any arguments and press return and the usage of the biopiece
- will be displayed.
- E.g.
-
-\series bold
-read_fasta
-\series default
- <return>:
-\end_layout
-
-\begin_layout Standard
-\begin_inset Box Frameless
-position "t"
-hor_pos "c"
-has_inner_box 1
-inner_pos "t"
-use_parbox 0
-width "100col%"
-special "none"
-height "1in"
-height_special "totalheight"
-status open
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Program name: read_fasta
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Contact: mail@maasha.dk
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Date: August 2007
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/
-gpl.html)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Description: Read FASTA entries.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Usage: read_fasta [options] -i <FASTA file(s)>
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Options:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-i <file(s)> | --data_in=<file(s)>] - Comma separated list of files
- to read.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-n <int> | --num=<int>] - Limit number of records to read.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-I <file> | --stream_in=<file>] - Read input stream from file
- - Default=STDIN
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-O <file> | --stream_out=<file>] - Write output stream to file
- - Default=STDOUT
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Examples:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i test.fna - Read FASTA entries from file.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i test1.fna,test2,fna - Read FASTA entries from files.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i '*.fna' - Read FASTA entries from files.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i test.fna -n 10 - Read first 10 FASTA entries from
- file.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Section
-The Data Stream
-\end_layout
-
-\begin_layout Subsection
-How to read the data stream from file?
-\begin_inset LatexCommand label
-name "sub:How-to-read-stream"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-You want to read a data stream that you previously have saved to file in
- biopieces format.
- This can be done implicetly or explicitly.
- The implicit way uses the 'stdout' stream of the Unix terminal:
-\end_layout
-
-\begin_layout LyX-Code
-cat | <biopiece>
-\end_layout
-
-\begin_layout Standard
-cat is the Unix command that reads a file and output the result to 'stdout'
- --- which in this case is piped to any biopiece represented by the <biopiece>.
- It is also possible to read the data stream using '<' to direct the 'stdout'
- stream into the biopiece like this:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> < <file>
-\end_layout
-
-\begin_layout Standard
-However, that will not work if you pipe more biopieces together.
- Then it is much safer to read the stream from a file explicitly like this:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --stream_in=<file>
-\end_layout
-
-\begin_layout Standard
-Here the filename <file> is explicetly given to the biopiece <biopiece>
- with the switch
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_in.
- This switch works with all biopieces.
- It is also possible to read in data from multiple sources by repeating
- the explicit read step:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --stream_in=<file1> | <biopiece> --stream_in=<file2>
-\end_layout
-
-\begin_layout Subsection
-How to write the data stream to file?
-\begin_inset LatexCommand label
-name "sub:How-to-write-stream"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-In order to save the output stream from a biopiece to file, so you can read
- in the stream again at a later time, you can do one of two things:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> > <file>
-\end_layout
-
-\begin_layout Standard
-All, the biopieces write the data stream to 'stdout' by default which can
- be written to a file by redirecting 'stdout' to file using '>' , however,
- if one of the biopieces for writing other formats is used then the both
- the biopieces records as well as the result output will go to 'stdout'
- in a mixture causing havock! To avoid this you must use the switch
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_out that explictly tells the biopiece to write the output stream
- to file:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --stream_out=<file>
-\end_layout
-
-\begin_layout Standard
-The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_out switch works with all biopieces.
-\end_layout
-
-\begin_layout Subsection
-How to terminate the data stream?
-\end_layout
-
-\begin_layout Standard
-The data stream is never stops unless the user want to save the stream or
- by supplying the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch that will terminate the stream:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --no_stream
-\end_layout
-
-\begin_layout Standard
-The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch only works with those biopieces where it makes sense that
- the user might want to terminale the data stream,
-\emph on
-i.e
-\emph default
-.
- after an analysis step where the user wants to output the result, but not
- the data stream.
-\end_layout
-
-\begin_layout Subsection
-How to write my results to file?
-\begin_inset LatexCommand label
-name "sub:How-to-write-result"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Saving the result of an analysis to file can be done implicitly or explicitly.
- The implicit way:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --no_stream > <file>
-\end_layout
-
-\begin_layout Standard
-If you use '>' to redirect 'stdout' to file then it is important to use
- the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch to avoid writing a mix of biopieces records and result
- to the same file causing havock.
- The safe way is to use the
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out switch which explicetly tells the biopiece to write the result
- to a given file:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --result_out=<file>
-\end_layout
-
-\begin_layout Standard
-Using the above method will not terminate the stream, so it is possible
- to pipe that into another biopiece generating different results:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece1> --result_out=<file1> | <biopiece2> --result_out=<file2>
-\end_layout
-
-\begin_layout Standard
-And still the data stream will continue unless terminated with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --result_out=<file> --no_stream
-\end_layout
-
-\begin_layout Standard
-Or written to file using implicitly or explicity
-\begin_inset LatexCommand eqref
-reference "sub:How-to-write-result"
-
-\end_inset
-
-.
- The explicit way:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --result_out=<file1> --stream_out=<file2>
-\end_layout
-
-\begin_layout Subsection
-How to read data from multiple sources?
-\end_layout
-
-\begin_layout Standard
-To read multiple data sources, with the same type or different type of data
- do:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece1> --data_in=<file1> | <biopiece2> --data_in=<file2>
-\end_layout
-
-\begin_layout Standard
-where type is the data type a specific biopiece reads.
-\end_layout
-
-\begin_layout Section
-Reading input
-\end_layout
-
-\begin_layout Subsection
-How to read biopieces input?
-\end_layout
-
-\begin_layout Standard
-See
-\begin_inset LatexCommand eqref
-reference "sub:How-to-read-stream"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Subsection
-How to read in data?
-\end_layout
-
-\begin_layout Standard
-Data in different formats can be read with the appropriate biopiece for
- that format.
- The biopieces are typicalled named 'read_<data type>' such as
-\series bold
-read_fasta
-\series default
-,
-\series bold
-read_bed
-\series default
-,
-\series bold
-read_tab
-\series default
-, etc., and all behave in a similar manner.
- Data can be read by supplying the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-data_in switch and a file name to the file containing the data:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --data_in=<file>
-\end_layout
-
-\begin_layout Standard
-It is also possible to read in a saved biopieces stream (see
-\begin_inset LatexCommand ref
-reference "sub:How-to-read-stream"
-
-\end_inset
-
-) as well as reading data in one go:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --stream_in=<file1> --data_in=<file2>
-\end_layout
-
-\begin_layout Standard
-If you want to read data from several files you can do this:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --data_in=<file1> | <biopiece> --data_in=<file2>
-\end_layout
-
-\begin_layout Standard
-If you have several data files you can read in all explicitly with a comma
- separated list:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --data_in=file1,file2,file3
-\end_layout
-
-\begin_layout Standard
-And it is also possible to use file globbing
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-using the short option will only work if you quote the argument -i '*.fna'
-\end_layout
-
-\end_inset
-
-:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --data_in=*.fna
-\end_layout
-
-\begin_layout Standard
-Or in a combination:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --data_in=file1,/dir/*.fna
-\end_layout
-
-\begin_layout Standard
-Finally, it is possible to read in data in different formats using the appropria
-te biopiece for each format:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece1> --data_in=<file1> | <biopiece2> --data_in=<file2> ...
-\end_layout
-
-\begin_layout Subsection
-How to read FASTA input?
-\end_layout
-
-\begin_layout Standard
-Sequences in FASTA format can be read explicitly using
-\series bold
-read_fasta
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file>
-\end_layout
-
-\begin_layout Subsection
-How to read alignment input?
-\end_layout
-
-\begin_layout Standard
-If your alignment if FASTA formatted then you can
-\series bold
-read_align
-\series default
-.
- It is also possible to use
-\series bold
-read_fasta
-\series default
- since the data is FASTA formatted, however, with
-\series bold
-read_fasta
-\series default
- the key ALIGN will be omitted.
- The ALIGN key is used to determine which sequences belong to what alignment
- which is required for
-\series bold
-write_align
-\series default
-.
-\end_layout
-
-\begin_layout LyX-Code
-read_align --data_in=<file>
-\end_layout
-
-\begin_layout Subsection
-How to read tabular input?
-\begin_inset LatexCommand label
-name "sub:How-to-read-table"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Tabular input can be read with
-\series bold
-read_tab
-\series default
- which will read in all rows and chosen columns (separated by a given delimter)
- from a table in text format.
-\end_layout
-
-\begin_layout Standard
-The table below:
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Tabular
-<lyxtabular version="3" rows="4" columns="3">
-<features>
-<column alignment="left" valignment="top" width="0">
-<column alignment="left" valignment="top" width="0">
-<column alignment="left" valignment="top" width="0">
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Human
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-ATACGTCAG
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-23524
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Dog
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-AGCATGAC
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-2442
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Mouse
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-GACTG
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-234
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Cat
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-AAATGCA
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-2342
-\end_layout
-
-\end_inset
-</cell>
-</row>
-</lyxtabular>
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Can be read using the command:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file>
-\end_layout
-
-\begin_layout Standard
-Which will result in four records, one for each row, where the keys V0,
- V1, V2 are the default keys for the organism, sequence, and count, respectively.
- It is possible to select a subset of colums to read by using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-cols switch which takes a comma separated list of columns numbers (first
- column is designated 0) as argument.
- So to read in only the sequence and the count so that the count comes before
- the sequence do:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file> --cols=2,1
-\end_layout
-
-\begin_layout Standard
-It is also possible to name the columns with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys switch:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file> --cols=2,1 --keys=COUNT,SEQ
-\end_layout
-
-\begin_layout Subsection
-How to read BED input?
-\end_layout
-
-\begin_layout Standard
-The BED (Browser Extensible Data
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://genome.ucsc.edu/FAQ/FAQformat"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-) format is a tabular format for data pertaining to one of the Eukaryotic
- genomes in the UCSC genome brower
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://genome.ucsc.edu/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-.
- The BED format consists of up to 12 columns, where the first three are
- mandatory CHR, CHR_BEG, and CHR_END.
- The mandatory columns and any of the optional columns can all be read in
- easily with the
-\series bold
-read_bed
-\series default
- biopiece.
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<file>
-\end_layout
-
-\begin_layout Standard
-It is also possible to read the BED file with
-\series bold
-read_tab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-read-table"
-
-\end_inset
-
-), however, that will be more cumbersome because you need to specify the
- keys:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file> --keys=CHR,CHR_BEG,CHR_END ...
-\end_layout
-
-\begin_layout Subsection
-How to read PSL input?
-\end_layout
-
-\begin_layout Standard
-The PSL format is the output from BLAT and contains 21 mandatory fields
- that can be read with
-\series bold
-read_psl
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-read_psl --data_in=<file>
-\end_layout
-
-\begin_layout Section
-Writing output
-\end_layout
-
-\begin_layout Standard
-All result output can be written explicitly to file using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out switch which all result generating biopieces have.
- It is also possible to write the result to file implicetly by directing
- 'stdout' to file using '>', however, that requires the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream swich to prevent a mixture of data stream and results in the file.
- The explicit (and safe) way:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | <biopiece> --result_out=<file>
-\end_layout
-
-\begin_layout Standard
-The implicit way:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | <biopiece> --no_stream > <file>
-\end_layout
-
-\begin_layout Subsection
-How to write biopieces output?
-\end_layout
-
-\begin_layout Standard
-See
-\begin_inset LatexCommand eqref
-reference "sub:How-to-write-stream"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Subsection
-How to write FASTA output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-fasta"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-FASTA output can be written with
-\series bold
-write_fasta
-\series default
-.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_fasta --result_out=<file>
-\end_layout
-
-\begin_layout Standard
-It is also possible to wrap the sequences to a given width using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-wrap switch allthough wrapping of sequence is generally an evil thing:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_fasta --no_stream --wrap=80
-\end_layout
-
-\begin_layout Subsection
-How to write alignment output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-alignment"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Pretty alignments with ruler
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-'.' for every 10 residues, ':' for every 50, and '|' for every 100
-\end_layout
-
-\end_inset
-
- and consensus sequence
-\begin_inset Note Note
-status collapsed
-
-\begin_layout Standard
-which reminds me to make that an option.
-\end_layout
-
-\end_inset
-
- can be created with
-\series bold
-write_align
-\series default
-, what also have the optional
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-wrap switch to break the alignment into blocks of a given width:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_align --result_out=<file> --wrap=80
-\end_layout
-
-\begin_layout Standard
-If the number of sequnces in the alignment is 2 then a pairwise alignment
- will be output otherwise a multiple alignment.
- And if the sequence type, determined automagically, is protein, then residues
- and symbols (+,\InsetSpace ~
-:,\InsetSpace ~
-.) will be used to show consensus according to the Blosum62
- matrix.
-\end_layout
-
-\begin_layout Subsection
-How to write tabular output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-tab"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Outputting the data stream as a table can be done with
-\series bold
-write_tab
-\series default
-, which will write generate one row per record with the values as columns.
- If you supply the optional
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-comment switch, when the first row in the table will be a 'comment' line
- prefixed with a '#':
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --comment
-\end_layout
-
-\begin_layout Standard
-You can also change the delimiter from the default (tab) to
-\emph on
-e.g.
-
-\emph default
- ',':
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --delimit=','
-\end_layout
-
-\begin_layout Standard
-If you want the values output in a specific order you have to supply a comma
- separated list using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys switch that will print only those keys in that order:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --keys=SEQ_NAME,COUNT
-\end_layout
-
-\begin_layout Standard
-Alternatively, if you have some keys that you don't want in the tabular
- output, use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_keys switch.
- So to print all keys except SEQ and SEQ_TYPE do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --no_keys=SEQ,SEQ_TYPE
-\end_layout
-
-\begin_layout Standard
-Finally, if you have a stream containing a mix of different records types,
-
-\emph on
-e.g.
-
-\emph default
- records with sequences and records with matches, then you can use
-\series bold
-write_tab
-\series default
- to output all the records in tabluar format, however, the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-comment,
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys, and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_keys switches will only respond to records of the first type encountered.
- The reason is that outputting mixed records is probably not what you want
- anyway, and you should remove all the unwanted records from the stream
- before outputting the table:
-\series bold
-grab
-\series default
- is your friend (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-grab"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to write a BED output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-BED"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Data in BED format can be output if the records contain the mandatory keys
- CHR, CHR_BEG, and CHR_END using
-\series bold
-write_bed
-\series default
-.
- If the optional keys are also present, they will be output as well:
-\end_layout
-
-\begin_layout LyX-Code
-write_bed --result_out=<file>
-\end_layout
-
-\begin_layout Subsection
-How to write PSL output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-PSL"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Data in PSL format can be output using
-\series bold
-write_psl:
-\end_layout
-
-\begin_layout LyX-Code
-write_psl --result_out=<file>
-\end_layout
-
-\begin_layout Section
-Manipulating Records
-\end_layout
-
-\begin_layout Subsection
-How to select a few records?
-\begin_inset LatexCommand label
-name "sub:How-to-select-a-few-records"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-To quickly get an overview of your data you can limit the data stream to
- show a few records.
- This also very useful to test the pipeline with a few records if you are
- setting up a complex analysis using several biopieces.
- That way you can inspect that all goes well before analyzing and waiting
- for the full data set.
- All of the read_<type> biopieces have the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num switch which will take a number as argument and only that number of
- records will be read.
- So to read in the first 10 FASTA entries from a file:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna --num=10
-\end_layout
-
-\begin_layout Standard
-Another way of doing this is to use
-\series bold
-head_records
-\series default
- will limit the stream to show the first 10 records (default):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | head_records
-\end_layout
-
-\begin_layout Standard
-Using
-\series bold
-head_records
-\series default
- directly after one of the read_<type> biopieces will be a lot slower than
- using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num switch with the read_<type> biopieces, however,
-\series bold
-head_records
-\series default
- can also be used to limit the output from all the other biopieces.
- It is also possible to give
-\series bold
-head_records
-\series default
- a number of records to show using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num switch.
- So to display the first 100 records do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | head_records --num=100
-\end_layout
-
-\begin_layout Subsection
-How to select random records?
-\begin_inset LatexCommand label
-name "sub:How-to-select-random-records"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-If you want to inspect a number of random records from the stream this can
- be done with the
-\series bold
-random_records
-\series default
- biopiece.
- So if you have 1 mio records in the stream and you want to select 1000
- random records do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | random_records --num=1000
-\end_layout
-
-\begin_layout Subsection
-How to count all records in the data stream?
-\end_layout
-
-\begin_layout Standard
-To count all the records in the data stream use
-\series bold
-count_records
-\series default
-, which adds one record (which is not included in the count) to the data
- stream.
- So to count the number of sequences in a FASTA file you can do this:
-\end_layout
-
-\begin_layout LyX-Code
-cat test.fna | read_fasta | count_records --no_stream
-\end_layout
-
-\begin_layout Standard
-Which will write the last record containing the count to 'stdout':
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_records: 630
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
----
-\end_layout
-
-\begin_layout Standard
-It is also possible to write the count to file using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out switch.
-\end_layout
-
-\begin_layout Subsection
-How to get the length of record values?
-\begin_inset LatexCommand label
-name "sub:How-to-get-value_length"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Use the
-\series bold
-length_vals
-\series default
- biopiece to get the length of each value for a comma separated list of
- keys:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | length_vals --keys=HIT,PATTERN
-\end_layout
-
-\begin_layout Subsection
-How to grab specific records?
-\begin_inset LatexCommand label
-name "sub:How-to-grab"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The biopiece
-\series bold
-grab
-\series default
- is related to the Unix grep and locates records based on matching keys
- and/or values using either a pattern, a Perl regex, or a numerical evaluation.
- To easily
-\series bold
-grab
-\series default
- all records in the stream that has any mentioning of the pattern 'human'
- just pipe the data stream through
-\series bold
-grab
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human
-\end_layout
-
-\begin_layout Standard
-This will search for the pattern 'human' in all keys and all values.
- The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern switch takes a comma separated list of patterns, so in order to
- match multiple patterns do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human,mouse
-\end_layout
-
-\begin_layout Standard
-It is also possible to use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in switch instead of
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern.
-
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in is used to read a file with one pattern per line:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern_in=patterns.txt
-\end_layout
-
-\begin_layout Standard
-If you want the opposite result --- to find all records that does not match
- the patterns, add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-invert switch, which not only works with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern switch, but also with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-regex and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-eval:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human --invert
-\end_layout
-
-\begin_layout Standard
-If you want to search the record keys only,
-\emph on
-e.g.
-
-\emph default
- to find all records containing the key SEQ you can add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys_only switch.
- This will prevent matching of SEQ in any record value, and in fact SEQ
- is a not uncommon peptide sequence you could get an unwanted record.
- Also, this will give an increase in speed since only the keys are searched:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=SEQ --keys_only
-\end_layout
-
-\begin_layout Standard
-However, if you are interested in finding the peptide sequence SEQ and not
- the SEQ key, just add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-vals_only switch instead:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=SEQ --vals_only
-\end_layout
-
-\begin_layout Standard
-Also, if you want to grab for certain key/value pairs you can supply a comma
- separated list of keys whos values will then be searched using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys switch.
- This is handy if your records contain large genomic sequences and you dont
- want to search the entire sequence for
-\emph on
-e.g.
-
-\emph default
- the organism name --- it is much faster to tell
-\series bold
-grab
-\series default
- which keys to search the value for:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human --keys=SEQ_NAME
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout Standard
-It is also possible to invoke flexible matching using regex (regular expressions
-) instead of simple pattern matching.
- In
-\series bold
-grab
-\series default
- the regex engine is Perl based and allows use of different type of wild
- cards, alternatives,
-\emph on
-etc
-\emph default
-
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://perldoc.perl.org/perlreref.html"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-.
- If you want to
-\series bold
-grab
-\series default
- records withs the sequence ATCG or GCTA you can do this:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --regex='ATCG|GCTA'
-\end_layout
-
-\begin_layout Standard
-Or if you want to find sequences beginning with ATCG:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --regex='^ATCG'
-\end_layout
-
-\begin_layout Standard
-You can also use
-\series bold
-grab
-\series default
- to locate records that fulfill a numerical property using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-eval switch witch takes an expression in three parts.
- The first part is the key that holds the value we want to evaluate, the
- second part holds one the six operators:
-\end_layout
-
-\begin_layout Enumerate
-Greater than: >
-\end_layout
-
-\begin_layout Enumerate
-Greater than or equal to: >=
-\end_layout
-
-\begin_layout Enumerate
-Less than: <
-\end_layout
-
-\begin_layout Enumerate
-Less than or equal to: <=
-\end_layout
-
-\begin_layout Enumerate
-Equal to: =
-\end_layout
-
-\begin_layout Enumerate
-Not equal to: !=
-\end_layout
-
-\begin_layout Enumerate
-String wise equal to: eq
-\end_layout
-
-\begin_layout Enumerate
-String wise not equal to: ne
-\end_layout
-
-\begin_layout Standard
-And finally comes the number used in the evaluation.
- So to
-\series bold
-grab
-\series default
- all records with a sequence length greater than 30:
-\end_layout
-
-\begin_layout LyX-Code
-...
- length_seq | grab --eval='SEQ_LEN > 30'
-\end_layout
-
-\begin_layout Standard
-If you want to locate all records containing the pattern 'human' and where
- the sequence length is greater that 30, you do this by running the stream
- through
-\series bold
-grab
-\series default
- twice:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern='human' | length_seq | grab --eval='SEQ_LEN > 30'
-\end_layout
-
-\begin_layout Standard
-Finally, it is possible to do fast matching of expressions from a file using
- the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-exact switch.
- Each of these expressions has to be matched exactly over the entrie length,
- which if useful if you have a file with accession numbers, that you want
- to locate in the stream:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --exact acc_no.txt | ...
-\end_layout
-
-\begin_layout Standard
-Using
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-exact is much faster than using
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in, because with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-exact the expression has to be complete matches, where
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in looks for subpatterns.
-\end_layout
-
-\begin_layout Standard
-NB! To get the best speed performance, use the most restrictive
-\series bold
-grab
-\series default
- first.
-\end_layout
-
-\begin_layout Subsection
-How to remove keys from records?
-\end_layout
-
-\begin_layout Standard
-To remove one or more specific keys from all records in the data stream
- use
-\series bold
-remove_keys
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | remove_keys --keys=SEQ,SEQ_NAME
-\end_layout
-
-\begin_layout Standard
-In the above example SEQ and SEQ_NAME will be removed from all records if
- they exists in these.
- If all keys are removed from a record, then the record will be removed.
-\end_layout
-
-\begin_layout Subsection
-How to rename keys in records?
-\end_layout
-
-\begin_layout Standard
-Sometimes you want to rename a record key,
-\emph on
-e.g.
-
-\emph default
- if you have read in a two column table with sequence name and sequence
- in each column (see
-\begin_inset LatexCommand ref
-reference "sub:How-to-read-table"
-
-\end_inset
-
-) without specifying the key names, then the sequence name will be called
- V0 and the sequence V1 as default in the
-\series bold
-read_tab
-\series default
- biopiece.
- To rename the V0 and V1 keys we need to run the stream through
-\series bold
-rename_keys
-\series default
- twice (one for each key to rename):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | rename_keys --keys=V0,SEQ_NAME | rename_keys --keys=V1,SEQ
-\end_layout
-
-\begin_layout Standard
-The first instance of
-\series bold
-rename_keys
-\series default
- replaces all the V0 keys with SEQ_NAME, and the second instance of
-\series bold
-rename_keys
-\series default
- replaces all the V1 keys with SEQ.
-
-\emph on
-Et viola
-\emph default
- the data can now be used in the biopieces that requires these keys.
-\end_layout
-
-\begin_layout Section
-Manipulating Sequences
-\end_layout
-
-\begin_layout Subsection
-How to get sequence lengths?
-\end_layout
-
-\begin_layout Standard
-The length for sequences in records can be determined with
-\series bold
-length_seq
-\series default
-, which adds the key SEQ_LEN to each record with the sequence length as
- the value.
- It also generates an extra record that is emitted last with the key TOTAL_SEQ_L
-EN showing the total length of all the sequences.
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_seq
-\end_layout
-
-\begin_layout Standard
-It is also possible to determine the sequence length using the generic tool
-
-\series bold
-length_vals
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-get-value_length"
-
-\end_inset
-
-, which determines the length of the values for a given list of keys:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_vals --keys=SEQ
-\end_layout
-
-\begin_layout Standard
-To obtain the total length of all sequences use
-\series bold
-sum_vals
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_vals --keys=SEQ
-\end_layout
-
-\begin_layout LyX-Code
-| sum_vals --keys=SEQ_LEN
-\end_layout
-
-\begin_layout Standard
-The biopiece
-\series bold
-analyze_seq
-\series default
- will also determine the length of each sequence (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-analyze"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to analyze sequence composition?
-\begin_inset LatexCommand label
-name "sub:How-to-analyze"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-If you want to find out the sequence type, composition, length, as well
- as GC content, indel content and proportions of soft and hard masked sequence,
- then use
-\series bold
-analyze_seq
-\series default
-.
- This handy biopiece will determine all these things per sequence from which
- it is easy to get an overview using the
-\series bold
-write_tab
-\series default
- biopiece to output a table (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-tab"
-
-\end_inset
-
-).
- So in order to determine the sequence composition of a FASTA file with
- just one entry containing the sequence 'ATCG' we just read the data with
-
-\series bold
-read_fasta
-\series default
- and run the output through
-\series bold
-analyze_seq
-\series default
- which will add the analysis to the record like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq ...
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:D: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-MIX_INDEX: 0.55
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:W: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:G: 16
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SOFT_MASK%: 63.75
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:B: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:V: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-HARD_MASK%: 0.00
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:H: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:S: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:N: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:.: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-GC%: 35.00
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:A: 8
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:Y: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:M: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:T: 44
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SEQ_TYPE: DNA
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:K: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:~: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SEQ: TTTCAGTTTGGGACGGAGTAAGGCCTTCCtttttttttttttttttttttttttttttgagaccgagtcttgctc
-tgtcg
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SEQ_LEN:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-80 RES:R: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:C: 12
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:-: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:U: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
----
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout Standard
-Now to make a table of how may As, Ts, Cs, and Gs you can add the following:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | analyze_seq | write_tab --keys=RES:A,RES:T,RES:C,RES:G
-\end_layout
-
-\begin_layout Standard
-Or if you want to see the proportions of hard and soft masked sequence:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | analyse_seq | write_tab --keys=HARD_MASK%,SOFT_MASK%
-\end_layout
-
-\begin_layout Standard
-If you have a stack of sequences in one file and you want to determine the
- mean GC content you can do it using the
-\series bold
-mean_vals
-\series default
- biopiece:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq | mean_vals --keys=GC%
-\end_layout
-
-\begin_layout Standard
-Or if you want the total count of Ns you can use
-\series bold
-sum_vals
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq | sum_vals --keys=RES:N
-\end_layout
-
-\begin_layout Standard
-The MIX_INDEX key is calculated as the count of the most common residue
- over the sequence length, and can be used as a cut-off for removing sequence
- tags consisting of mostly one nucleotide:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq | grab --eval='MIX_INDEX<0.85'
-\end_layout
-
-\begin_layout Subsection
-How to extract subsequences?
-\begin_inset LatexCommand label
-name "sub:How-to-extract"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-In order to extract a subsequence from a longer sequence use the biopiece
- extract_seq, which will replace the sequence in the record with the subsequence
- (this behaviour should probably be modified to be dependant of a
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-replace or a
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_replace switch
-\begin_inset Note Note
-status collapsed
-
-\begin_layout Standard
-also in split_seq
-\end_layout
-
-\end_inset
-
-).
- So to extract the first 20 residues from all sequences do (first residue
- is designated 1):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | extract_seq --beg=1 --len=20
-\end_layout
-
-\begin_layout Standard
-You can also specify a begin and end coordinate set:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | extract_seq --beg=20 --end=40
-\end_layout
-
-\begin_layout Standard
-If you want the subsequences from position 20 to the sequence end do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | extract_seq --beg=20
-\end_layout
-
-\begin_layout Standard
-If you want to extract subsequences a given distance from the sequence end
- you can do this by reversing the sequence with the biopiece
-\series bold
-reverse_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-reverse-seq"
-
-\end_inset
-
-, followed by
-\series bold
-extract_seq
-\series default
- to get the subsequence, and then
-\series bold
-reverse_seq
-\series default
- again to get the subsequence back in the original orientation:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | reverse_seq
-\end_layout
-
-\begin_layout LyX-Code
-| extract_seq --beg=10 --len=10 | reverse_seq
-\end_layout
-
-\begin_layout Subsection
-How to get genomic sequence?
-\begin_inset LatexCommand label
-name "sub:How-to-get-genomic-sequence"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The biopiece
-\series bold
-get_genomic_seq
-\series default
- can extract subsequences for a given genome specified with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-genome switch explicitly using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-beg and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-end/
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-len switches:
-\end_layout
-
-\begin_layout LyX-Code
-get_genome_seq --genome=<genome> --beg=1 --len=100
-\end_layout
-
-\begin_layout Standard
-Alternatively,
-\series bold
-get_genome_seq
-\series default
- can be used to append the corresponding sequence to BED, PSL, and BLAST
- records:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<BED file> | get_genome_seq --genome=<genome>
-\end_layout
-
-\begin_layout Standard
-It is also possible to include flaking sequence using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-flank switch.
- So to include 50 nucleotides upstream and 50 nucleotides downstream for
- each BED entry do:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<BED file> | get_genome_seq --genome=<genome> --flank=50
-\end_layout
-
-\begin_layout Subsection
-How to upper-case sequences?
-\end_layout
-
-\begin_layout Standard
-Sequences can be shifted from lower case to upper case using
-\series bold
-uppercase_seq
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | uppercase_seq
-\end_layout
-
-\begin_layout Subsection
-How to reverse sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-reverse-seq"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The order of residues in a sequence can be reversed using reverse_seq:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | reverse_seq
-\end_layout
-
-\begin_layout Standard
-Note that in order to reverse/complement a sequence you also need the
-\series bold
-complement_seq
-\series default
- biopiece (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-complement"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to complement sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-complement"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-DNA and RNA sequences can be complemented with
-\series bold
-complement_seq
-\series default
-, which automagically determines the sequence type:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | complement_seq
-\end_layout
-
-\begin_layout Standard
-Note that in order to reverse/complement a sequence you also need the
-\series bold
-reverse_seq
-\series default
- biopiece (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-reverse-seq"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to remove indels from sequnces?
-\end_layout
-
-\begin_layout Standard
-Indels can be removed from sequences with the
-\series bold
-remove_indels
-\series default
- biopiece.
- This is useful if you have aligned some sequences (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-align"
-
-\end_inset
-
-) and extracted (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-extract"
-
-\end_inset
-
-) a block of subsequences from the alignment and you want to use these sequence
- in a search where you need to remove the indels first.
- '-', '~', and '.' are considered indels:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | remove_indels
-\end_layout
-
-\begin_layout Subsection
-How to shuffle sequences?
-\end_layout
-
-\begin_layout Standard
-All residues in sequences in the stream can be shuffled to random positions
- using the
-\series bold
-shuffle_seq
-\series default
- biopiece:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | shuffle_seq
-\end_layout
-
-\begin_layout Subsection
-How to split sequences into overlapping subsequences?
-\end_layout
-
-\begin_layout Standard
-Sequences can be slit into overlapping subsequences with the
-\series bold
-split_seq
-\series default
- biopiece.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | split_seq --word_size=20 --uniq
-\end_layout
-
-\begin_layout Subsection
-How to determine the oligo frequency?
-\end_layout
-
-\begin_layout Standard
-In order to determine if any oligo usage is over represented in one or more
- sequences you can determine the frequency of oligos of a given size with
-
-\series bold
-oligo_freq
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | oligo_freq --word_size=4
-\end_layout
-
-\begin_layout Standard
-And if you have more than one sequence and want to accumulate the frequences
- you need the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-all switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | oligo_freq --word_size=4 --all
-\end_layout
-
-\begin_layout Standard
-To get a meaningful result you need to write the resulting frequencies as
- a table with
-\series bold
-write_tab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-tab"
-
-\end_inset
-
-), but first it is important to
-\series bold
-grab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-grab"
-
-\end_inset
-
-) the records with the frequencies to avoid full length sequences in the
- table:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | oligo_freq --word_size=4 --all | grab --pattern=OLIGO --keys_only
-\end_layout
-
-\begin_layout LyX-Code
-| write_tab --no_stream
-\end_layout
-
-\begin_layout Standard
-And the resulting frequency table can be sorted with Unix sort (man sort).
-\end_layout
-
-\begin_layout Subsection
-How to search for sequences in genomes?
-\end_layout
-
-\begin_layout Standard
-See the following biopiece:
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-patscan_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-patscan"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-blat_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAT"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-blast_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAST"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-vmatch_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-Vmatch"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to search sequences for a pattern?
-\begin_inset LatexCommand label
-name "sub:How-to-use-patscan"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-It is possible to search sequences in the data stream for patterns using
- the
-\series bold
-patscan_seq
-\series default
- biopiece which utilizes the powerful scan_for_matches engine.
- Consult the documentation for scan_for_matches in order to learn how to
- define patterns (the documentation is included in Appendix\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sec:scan_for_matches-README"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Standard
-To search all sequences for a simple pattern consisting of the sequence
- ATCGATCG allowing for 3 mismatches, 2 insertions and 1 deletion:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | patscan_seq --pattern='ATCGATCG[3,2,1]'
-\end_layout
-
-\begin_layout Standard
-The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern switch takes a comma seperated list of patterns, so if you want
- to search for more that one pattern do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern='ATCGATCG[3,2,1],GCTAGCTA[3,2,1]'
-\end_layout
-
-\begin_layout Standard
-It is also possible to have a list of different patterns to search for in
- a file with one pattern per line.
- In order to get
-\series bold
-patscan_seq
-\series default
- to read these patterns use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern_in=<file>
-\end_layout
-
-\begin_layout Standard
-To also scan the complementary strand in nucleotide sequences (
-\series bold
-patscan_seq
-\series default
- automagically determines the sequence type) you need to add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-comp switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern=<pattern> --comp
-\end_layout
-
-\begin_layout Standard
-It is also possible to use
-\series bold
-patscan_seq
-\series default
- to output those records that does not contain a certain pattern by using
- the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-invert switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern=<pattern> --invert
-\end_layout
-
-\begin_layout Standard
-Finally,
-\series bold
-patscan_seq
-\series default
- can also scan for patterns in a given genome sequence, instead of sequences
- in the stream, using the
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-genome switch:
-\end_layout
-
-\begin_layout LyX-Code
-patscan --pattern=<pattern> --genome=<genome>
-\end_layout
-
-\begin_layout Subsection
-How to use BLAT for sequence search?
-\begin_inset LatexCommand label
-name "sub:How-to-use-BLAT"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Sequences in the data stream can be matched against supported genomes using
-
-\series bold
-blat_seq
-\series default
- which is a biopiece using BLAT as the name might suggest.
- Currently only Mouse and Human genomes are available and it is not possible
- to use OOC files since there is still a need for a local repository for
- genome files.
- Otherwise it is just:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | blat_seq --genome=<genome>
-\end_layout
-
-\begin_layout Standard
-The search results can then be written to file with
-\series bold
-write_psl
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-PSL"
-
-\end_inset
-
-) or
-\series bold
-write_bed
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-BED"
-
-\end_inset
-
-) allthough with
-\series bold
-write_bed
-\series default
- some information will be lost).
- It is also possible to plot chromosome distribution of the search results
- using
-\series bold
-plot_chrdist
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-plot-chrdist"
-
-\end_inset
-
-) or the distribution of the match lengths using
-\series bold
-plot_lendist
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-plot-lendist"
-
-\end_inset
-
-) or a karyogram with the hits using
-\series bold
-plot_karyogram
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-plot-karyogram"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to use BLAST for sequence search?
-\begin_inset LatexCommand label
-name "sub:How-to-use-BLAST"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Two biopieces exist for blasting sequences:
-\series bold
-create_blast_db
-\series default
- is used to create the BLAST database required for BLAST which is queried
- using the biopiece
-\series bold
-blast_seq
-\series default
-.
- So in order to create a BLAST database from sequences in the data stream
- you simple run:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_blast_db --database=my_database --no_stream
-\end_layout
-
-\begin_layout Standard
-The type of sequence to use for the database is automagically determined
- by
-\series bold
-create_blast_db
-\series default
-, but don't have a mixture of peptide and nucleic acids sequences in the
- stream.
- The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-database switch takes a path as argument, but will default to 'blastdb_<time_sta
-mp> if not set.
-\end_layout
-
-\begin_layout Standard
-The resulting database can now be queried with sequences in another data
- stream using
-\series bold
-blast_seq
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | blast_seq --database=my_database
-\end_layout
-
-\begin_layout Standard
-Again, the sequence type is determined automagically and the appropriate
- BLAST program is guessed (see below table), however, the program name can
- be overruled with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-program switch.
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Tabular
-<lyxtabular version="3" rows="5" columns="3">
-<features>
-<column alignment="center" valignment="top" width="0">
-<column alignment="center" valignment="top" width="0">
-<column alignment="center" valignment="top" width="0">
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Subject sequence
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Query sequence
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Program guess
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-blastn
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-blastp
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-blastx
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-tblastn
-\end_layout
-
-\end_inset
-</cell>
-</row>
-</lyxtabular>
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Finally, it is also possible to use
-\series bold
-blast_seq
-\series default
- for blasting sequences agains a preformatted genome using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-genome switch instead of the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-database switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | blast_seq --genome=<genome>
-\end_layout
-
-\begin_layout Subsection
-How to use Vmatch for sequence search?
-\begin_inset LatexCommand label
-name "sub:How-to-use-Vmatch"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The powerful suffix array software package Vmatch
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://www.vmatch.de/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
- can be used for exact mapping of sequences against indexed genomes using
- the biopiece
-\series bold
-vmatch_seq
-\series default
-, which will e.g.
- map 700000 ESTs to the human genome locating all 160 mio hits in less than
- an hour.
- Only nucleotide sequences and sequences longer than 11 nucleotides will
- be mapped.
- It is recommended that sequences consisting of mostly one nucleotide type
- are removed.
- This can be done with the
-\series bold
-analyze_seq
-\series default
- biopiece
-\begin_inset LatexCommand eqref
-reference "sub:How-to-analyze"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome>
-\end_layout
-
-\begin_layout Standard
-It is also possible to allow for mismatches using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-hamming_dist switch.
- So to allow for 2 mismatches:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=2
-\end_layout
-
-\begin_layout Standard
-Or to allow for 10% mismathing nucleotides:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=10p
-\end_layout
-
-\begin_layout Standard
-To allow both indels and mismatches use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-edit_dist switch.
- So to allow for one mismatch or one indel:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=1
-\end_layout
-
-\begin_layout Standard
-Or to allow for 5% indels or mismatches:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=5p
-\end_layout
-
-\begin_layout Standard
-Note that using
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-hamming_dist or
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-edit_dist greatly slows down vmatch considerably --- use with care.
-\end_layout
-
-\begin_layout Standard
-The resulting SCORE key can be replaced to hold the number of genome matches
- of a given sequence (multi-mappers) is the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-count switch is given.
-\end_layout
-
-\begin_layout Subsection
-How to find all matches between sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-find-matches"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-All matches between two sequences can be determined with the biopiece
-\series bold
-match_seq
-\series default
-.
- The match finding engine underneath the hood of
-\series bold
-match_seq
-\series default
- is the super fast suffix tree program MUMmer
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://mummer.sourceforge.net/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-, which will locate all forward and reverse matches between huge sequences
- in a matter of minutes (if the repeat count is not too high and if the
- word size used is appropriate).
- Matching two
-\emph on
-Helicobacter pylori
-\emph default
- genomes (1.7Mbp) takes around 10 seconds:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | match_seq --word_size=20 --direction=both
-\end_layout
-
-\begin_layout Standard
-The output from
-\series bold
-match_seq
-\series default
- can be used to generate a dot plot with
-\series bold
-plot_matches
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-generate-dotplot"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to align sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-align"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Sequences in the stream can be aligned with the
-\series bold
-align_seq
-\series default
- biopiece that uses Muscle
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://www.drive5.com/muscle/muscle.html"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
- as aligment engine.
- Currently you cannot change any of the Muscle alignment parameters and
-
-\series bold
-align_seq
-\series default
- will create an alignment based on the defaults (which are really good!):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | align_seq
-\end_layout
-
-\begin_layout Standard
-The aligned output can be written to file in FASTA format using
-\series bold
-write_fasta
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-fasta"
-
-\end_inset
-
-) or in pretty text using
-\series bold
-write_align
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-alignment"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to create a weight matrix?
-\end_layout
-
-\begin_layout Standard
-If you want a weight matrix to show the sequence composition of a stack
- of sequences you can use the biopiece create_weight_matrix:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_weight_matrix
-\end_layout
-
-\begin_layout Standard
-The result can be output in percent using the
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-percent switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_weight_matrix --percent
-\end_layout
-
-\begin_layout Standard
-The weight matrix can be written as tabular output with
-\series bold
-write_tab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-tab"
-
-\end_inset
-
-) after removeing the records containing SEQ with
-\series bold
-grab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-grab"
-
-\end_inset
-
-):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_weight_matrix | grab --invert --keys=SEQ --keys_only
-\end_layout
-
-\begin_layout LyX-Code
-| write_tab --no_stream
-\end_layout
-
-\begin_layout Standard
-The V0 column will hold the residue, while the rest of the columns will
- hold the frequencies for each sequence position.
-\end_layout
-
-\begin_layout Section
-Plotting
-\end_layout
-
-\begin_layout Standard
-There exists several biopieces for plotting.
- Some of these are based on GNUplot
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://www.gnuplot.info/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-, which is an extremely powerful platform to generate all sorts of plots
- and even though GNUplot has quite a steep learning curve, the biopieces
- utilizing GNUplot are simple to use.
- GNUplot is able to output a lot of different formats (called terminals
- in GNUplot), but the biopieces focusses on three formats only:
-\end_layout
-
-\begin_layout Enumerate
-The 'dumb' terminal is default to the GNUplot based biopieces and will output
- a plot in crude ASCII text (Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Dumb-terminal"
-
-\end_inset
-
-).
- This is quite nice for a quick and dirty plot to get an overview of your
- data .
-\end_layout
-
-\begin_layout Enumerate
-The 'post' or 'postscript' terminal output postscript code which is publication
- grade graphics that can be viewed with applications such as Ghostview,
- Photoshop, and Preview.
-\end_layout
-
-\begin_layout Enumerate
-The 'svg' terminal output's scalable vector graphics (SVG) which is a vector
- based format.
- SVG is great because you can edit the resulting plot using Photoshop or
- Inkscape
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-Inkscape is a really handy drawing program that is free and open source.
- Availble at
-\begin_inset LatexCommand htmlurl
-target "http://www.inkscape.org"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
- if you want to add additional labels, captions, arrows, and so on and then
- save the result in different formats, such as postscript without loosing
- resolution.
-\end_layout
-
-\begin_layout Standard
-The biopieces for plotting that are not based on GNUplot only output SVG
- (that may change in the future).
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename lendist_ascii.png
- lyxscale 70
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Dumb-terminal"
-
-\end_inset
-
-Dumb terminal
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-The output of a length distribution plot in the default 'dumb terminal'
- to the terminal window.
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a histogram?
-\begin_inset LatexCommand label
-name "How-to-plot-histogram"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-A generic histogram for a given value can be plotted with the biopiece
-\series bold
-plot_histogram
-\series default
- (Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Histogram"
-
-\end_inset
-
-):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_histogram --key=TISSUE --no_stream
-\end_layout
-
-\begin_layout Standard
-(Figure missing)
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align left
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename histogram.png
- lyxscale 70
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Histogram"
-
-\end_inset
-
-Histogram
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a length distribution?
-\begin_inset LatexCommand label
-name "sub:How-to-plot-lendist"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Plotting of length distributions, weather sequence lengths, patterns lengths,
- hit lengths,
-\emph on
-etc.
-
-\emph default
- is a really handy thing and can be done with the the biopiece
-\series bold
-plot_lendist
-\series default
-.
- If you have a file with FASTA entries and want to plot the length distribution
- you do it like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_seq
-\end_layout
-
-\begin_layout LyX-Code
-| plot_lendist --key=SEQ_LEN --no_stream
-\end_layout
-
-\begin_layout Standard
-The result will be written to the default dumb terminal and will look like
- Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Dumb-terminal"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-If you instead want the result in postscript format you can do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_lendist --key=SEQ_LEN --terminal=post --result_out=file.ps
-\end_layout
-
-\begin_layout Standard
-That will generate the plot and save it to file, but not interrupt the data
- stream which can then be used in further analysis.
- You can also save the plot implicetly using '>', however, it is then important
- to terminate the stream with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_lendist --key=SEQ_LEN --terminal=post --no_stream > file.ps
-\end_layout
-
-\begin_layout Standard
-The resulting plot can be seen in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Length-distribution"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename lendist.ps
- lyxscale 50
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Length-distribution"
-
-\end_inset
-
-Length distribution
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-Length distribution of 630 piRNA like RNAs.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a chromosome distribution?
-\begin_inset LatexCommand label
-name "sub:How-to-plot-chrdist"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-If you have the result of a sequence search against a multi chromosome genome,
- it is very practical to be able to plot the distribution of search hits
- on the different chromosomes.
- This can be done with
-\series bold
-plot_chrdist
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | blat_genome | plot_chrdist --no_stream
-\end_layout
-
-\begin_layout Standard
-The above example will result in a crude plot using the 'dumb' terminal,
- and if you want to mess around with the results from the BLAT search you
- probably want to save the result to file first (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-PSL"
-
-\end_inset
-
-).
- To plot the chromosome distribution from the saved search result you can
- do:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=file.bed | plot_chrdist --terminal=post --result_out=plot.ps
-\end_layout
-
-\begin_layout Standard
-That will result in the output show in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Chromosome-distribution"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename chrdist.ps
- lyxscale 50
- width 12cm
- rotateAngle 90
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Chromosome-distribution"
-
-\end_inset
-
-Chromosome distribution
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to generate a dotplot?
-\begin_inset LatexCommand label
-name "sub:How-to-generate-dotplot"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-A dotplot is a powerful way to get an overview of the size and location
- of sequence insertions, deletions, and duplications between two sequences.
- Generating a dotplot with biopieces is a two step process where you initially
- find all matches between two sequences using the tool
-\series bold
-match_seq
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-find-matches"
-
-\end_inset
-
-) and plot the resulting matches with
-\series bold
-plot_matches
-\series default
-.
- Matching and plotting two
-\emph on
-Helicobacter pylori
-\emph default
- genomes (1.7Mbp) takes around 10 seconds:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | match_seq | plot_matches --terminal=post --result_out=plot.ps
-\end_layout
-
-\begin_layout Standard
-The resulting dotplot is in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Dotplot"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename dotplot.ps
- lyxscale 50
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Dotplot"
-
-\end_inset
-
-Dotplot
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-Forward matches are displayed in green while reverse matches are displayed
- in red.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a sequence logo?
-\end_layout
-
-\begin_layout Standard
-Sequence logos can be generate with
-\series bold
-plot_seqlogo
-\series default
-.
- The sequnce type is determined automagically and an entropy scale of 2
- bits and 4 bits is used for nucleotide and peptide sequences, respectively
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand htmlurl
-target "http://www.ccrnp.ncifcrf.gov/~toms/paper/hawaii/latex/node5.html"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_seqlogo --no_stream --result_out=seqlogo.svg
-\end_layout
-
-\begin_layout Standard
-An example of a sequence logo can be seen in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Sequence-logo"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename seqlogo.png
- lyxscale 50
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Sequence-logo"
-
-\end_inset
-
-Sequence logo
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a karyogram?
-\begin_inset LatexCommand label
-name "sub:How-to-plot-karyogram"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-To plot search hits on genomes use
-\series bold
-plot_karyogram
-\series default
-, which will output a nice karyogram in SVG graphics:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_karyogram --result_out=karyogram.svg
-\end_layout
-
-\begin_layout Standard
-The banding data is taken from the UCSC genome browser database and currently
- only Human and Mouse is supported.
- Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Karyogram"
-
-\end_inset
-
- shows the distribution of piRNA like RNAs matched to the Human genome.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename karyogram.png
- lyxscale 35
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Karyogram"
-
-\end_inset
-
-Karyogram
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-Hits from a search of piRNA like RNAs in the Human genome is displayed as
- short horizontal bars.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Section
-Uploading Results
-\end_layout
-
-\begin_layout Subsection
-How do I display my results in the UCSC Genome Browser?
-\end_layout
-
-\begin_layout Standard
-Results from the list of biopieces below can be uploaded directly to a local
- mirror of the UCSC Genome Browser using the biopiece
-\series bold
-upload_to_ucsc
-\series default
-:
-\end_layout
-
-\begin_layout Itemize
-patscan_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-patscan"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-blat_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAT"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-blast_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAST"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-vmatch_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-Vmatch"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The syntax for uploading data the most simple way requires two mandatory
- switches:
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-database, which is the UCSC database name (such as hg18, mm9, etc.) and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-table which should be the users initials followed by an underscore and a
- short description of the data:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | upload_to_ucsc --database=hg18 --table=mah_snoRNAs
-\end_layout
-
-\begin_layout Standard
-The
-\series bold
-upload_to_ucsc
-\series default
- biopiece modifies the users ~/ucsc/my_tracks.ra file automagically (a backup
- is created with the name ~/ucsc/my_tracks.ra~) with default values that
- can be overridden using the following switches:
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-short_label - Short label for track - Default=database->table
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-long_label - Long label for track - Default=database->table
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-group - Track group name - Default=<user name as defined in env>
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-priority - Track display priority - Default=1
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-color - Track color - Default=147,73,42
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-chunk_size - Chunks for loading - Default=10000000
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-visibility - Track visibility - Default=pack
-\end_layout
-
-\begin_layout Standard
-Also, data in BED or PSL format can be uploaded with
-\series bold
-upload_to_ucsc
-\series default
- as long as these reference to genomes and chromosomes existing in the UCSC
- Genome Browser:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<bed file> | upload_to_ucsc ...
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-read_psl --data_in=<psl file> | upload_to_ucsc ...
-\end_layout
-
-\begin_layout Section
-Power Scripting
-\end_layout
-
-\begin_layout Standard
-It is possible to do commandline scripting of biopiece records using Perl.
- Because a biopiece record essentially is a hash structure, you can pass
- records to
-\series bold
-bioscript
-\series default
- command, which is a wrapper around the Perl executable that allows direct
- manipulations of the records using the power of Perl.
-\end_layout
-
-\begin_layout Standard
-In the below example we replace in all records the value to the CHR key
- with a forthrunning number:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | bioscript 'while($r=get_record(
-\backslash
-*STDIN)){$r->{CHR}=$i++; put_record($r)}'
-\end_layout
-
-\begin_layout Standard
-Something more useful would probably be to create custom FASTA headers.
- E.g.
- if we read in a BED file, lookup the genomic sequence, create a custom
- FASTA header with
-\series bold
-bioscript
-\series default
- and output FASTA entries:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | bioscript 'while($r=get_record(
-\backslash
-*STDIN)){$r->{SEQ_NAME}= //
-\end_layout
-
-\begin_layout LyX-Code
-join("_",$r->{CHR},$r->{CHR_BEG},$r->{CHR_END}); put_record($r)}'
-\end_layout
-
-\begin_layout Standard
-And the output:
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_21567527_21567550
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_693380_693403
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_13859534_13859557
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_9005090_9005113
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_2106825_2106848
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_14649031_14649054
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout Section
-Trouble shooting
-\end_layout
-
-\begin_layout Standard
-Shoot the messenger!
-\end_layout
-
-\begin_layout Section
-\start_of_appendix
-Keys
-\begin_inset LatexCommand label
-name "sec:Keys"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-HIT
-\end_layout
-
-\begin_layout Standard
-HIT_BEG
-\end_layout
-
-\begin_layout Standard
-HIT_END
-\end_layout
-
-\begin_layout Standard
-HIT_LEN
-\end_layout
-
-\begin_layout Standard
-HIT_NAME
-\end_layout
-
-\begin_layout Standard
-PATTERN
-\end_layout
-
-\begin_layout Section
-Switches
-\begin_inset LatexCommand label
-name "sec:Switches"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_in
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_out
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-data_in
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num
-\end_layout
-
-\begin_layout Section
-scan_for_matches README
-\begin_inset LatexCommand label
-name "sec:scan_for_matches-README"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches:
-\end_layout
-
-\begin_layout LyX-Code
- A Program to Scan Nucleotide or Protein Sequences for Matching Patterns
-\end_layout
-
-\begin_layout LyX-Code
- Ross Overbeek
-\end_layout
-
-\begin_layout LyX-Code
- MCS
-\end_layout
-
-\begin_layout LyX-Code
- Argonne National Laboratory
-\end_layout
-
-\begin_layout LyX-Code
- Argonne, IL 60439
-\end_layout
-
-\begin_layout LyX-Code
- USA
-\end_layout
-
-\begin_layout LyX-Code
-Scan_for_matches is a utility that we have written to search for
-\end_layout
-
-\begin_layout LyX-Code
-patterns in DNA and protein sequences.
- I wrote most of the code,
-\end_layout
-
-\begin_layout LyX-Code
-although David Joerg and Morgan Price wrote sections of an
-\end_layout
-
-\begin_layout LyX-Code
-earlier version.
- The whole notion of pattern matching has a rich
-\end_layout
-
-\begin_layout LyX-Code
-history, and we borrowed liberally from many sources.
- However, it is
-\end_layout
-
-\begin_layout LyX-Code
-worth noting that we were strongly influenced by the elegant tools
-\end_layout
-
-\begin_layout LyX-Code
-developed and distributed by David Searls.
- My intent is to make the
-\end_layout
-
-\begin_layout LyX-Code
-existing tool available to anyone in the research community that might
-\end_layout
-
-\begin_layout LyX-Code
-find it useful.
- I will continue to try to fix bugs and make suggested
-\end_layout
-
-\begin_layout LyX-Code
-enhancements, at least until I feel that a superior tool exists.
-\end_layout
-
-\begin_layout LyX-Code
-Hence, I would appreciate it if all bug reports and suggestions are
-\end_layout
-
-\begin_layout LyX-Code
-directed to me at Overbeek@mcs.anl.gov.
-
-\end_layout
-
-\begin_layout LyX-Code
-I will try to log all bug fixes and report them to users that send me
-\end_layout
-
-\begin_layout LyX-Code
-their email addresses.
- I do not require that you give me your name
-\end_layout
-
-\begin_layout LyX-Code
-and address.
- However, if you do give it to me, I will try to notify
-\end_layout
-
-\begin_layout LyX-Code
-you of serious problems as they are discovered.
-\end_layout
-
-\begin_layout LyX-Code
-Getting Started:
-\end_layout
-
-\begin_layout LyX-Code
- The distribution should contain at least the following programs:
-\end_layout
-
-\begin_layout LyX-Code
- README - This document
-\end_layout
-
-\begin_layout LyX-Code
- ggpunit.c - One of the two source files
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches.c - The second source file
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- run_tests - A perl script to test things
-\end_layout
-
-\begin_layout LyX-Code
- show_hits - A handy perl script
-\end_layout
-
-\begin_layout LyX-Code
- test_dna_input - Test sequences for DNA
-\end_layout
-
-\begin_layout LyX-Code
- test_dna_patterns - Test patterns for DNA scan
-\end_layout
-
-\begin_layout LyX-Code
- test_output - Desired output from test
-\end_layout
-
-\begin_layout LyX-Code
- test_prot_input - Test protein sequences
-\end_layout
-
-\begin_layout LyX-Code
- test_prot_patterns - Test patterns for proteins
-\end_layout
-
-\begin_layout LyX-Code
- testit - a perl script used for test
-\end_layout
-
-\begin_layout LyX-Code
- Only the first three files are required.
- The others are useful,
-\end_layout
-
-\begin_layout LyX-Code
- but only if you have Perl installed on your system.
- If you do
-\end_layout
-
-\begin_layout LyX-Code
- have Perl, I suggest that you type
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- which perl
-\end_layout
-
-\begin_layout LyX-Code
- to find out where it installed.
- On my system, I get the following
-\end_layout
-
-\begin_layout LyX-Code
- response:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- clone% which perl
-\end_layout
-
-\begin_layout LyX-Code
- /usr/local/bin/perl
-\end_layout
-
-\begin_layout LyX-Code
- indicating that Perl is installed in /usr/local/bin.
- Anyway, once
-\end_layout
-
-\begin_layout LyX-Code
- you know where it is installed, edit the first line of files
-\end_layout
-
-\begin_layout LyX-Code
- testit
-\end_layout
-
-\begin_layout LyX-Code
- show_hits
-\end_layout
-
-\begin_layout LyX-Code
- replacing /usr/local/bin/perl with the appropriate location.
- I
-\end_layout
-
-\begin_layout LyX-Code
- will assume that you can do this, although it is not critical (it
-\end_layout
-
-\begin_layout LyX-Code
- is needed only to test the installation and to use the "show_hits"
-\end_layout
-
-\begin_layout LyX-Code
- utility).
- Perl is not required to actually install and run
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches.
-
-\end_layout
-
-\begin_layout LyX-Code
- If you do not have Perl, I suggest you get it and install it (it
-\end_layout
-
-\begin_layout LyX-Code
- is a wonderful utility).
- Information about Perl and how to get it
-\end_layout
-
-\begin_layout LyX-Code
- can be found in the book "Programming Perl" by Larry Wall and
-\end_layout
-
-\begin_layout LyX-Code
- Randall L.
- Schwartz, published by O'Reilly & Associates, Inc.
-\end_layout
-
-\begin_layout LyX-Code
- To get started, you will need to compile the program.
- I do this
-\end_layout
-
-\begin_layout LyX-Code
- using
-\end_layout
-
-\begin_layout LyX-Code
- gcc -O -o scan_for_matches ggpunit.c scan_for_matches.c
-\end_layout
-
-\begin_layout LyX-Code
- If you do not use GNU C, use
-\end_layout
-
-\begin_layout LyX-Code
- cc -O -DCC -o scan_for_matches ggpunit.c scan_for_matches.c
-\end_layout
-
-\begin_layout LyX-Code
- which works on my Sun.
-
-\end_layout
-
-\begin_layout LyX-Code
- Once you have compiled scan_for_matches, you can verify that it
-\end_layout
-
-\begin_layout LyX-Code
- works with
-\end_layout
-
-\begin_layout LyX-Code
- clone% run_tests tmp
-\end_layout
-
-\begin_layout LyX-Code
- clone% diff tmp test_output
-\end_layout
-
-\begin_layout LyX-Code
- You may get a few strange lines of the sort
-\end_layout
-
-\begin_layout LyX-Code
- clone% run_tests tmp
-\end_layout
-
-\begin_layout LyX-Code
- rm: tmp: No such file or directory
-\end_layout
-
-\begin_layout LyX-Code
- clone% diff tmp test_output
-\end_layout
-
-\begin_layout LyX-Code
- These should cause no concern.
- However, if the "diff" shows that
-\end_layout
-
-\begin_layout LyX-Code
- tmp and test_output are different, contact me (you have a
-\end_layout
-
-\begin_layout LyX-Code
- problem).
-
-\end_layout
-
-\begin_layout LyX-Code
- You should now be able to use scan_for_matches by following the
-\end_layout
-
-\begin_layout LyX-Code
- instructions given below (which is all the normal user should have
-\end_layout
-
-\begin_layout LyX-Code
- to understand, once things are installed properly).
-\end_layout
-
-\begin_layout LyX-Code
- ==============================================================
-\end_layout
-
-\begin_layout LyX-Code
-How to run scan_for_matches:
-\end_layout
-
-\begin_layout LyX-Code
- To run the program, you type need to create two files
-\end_layout
-
-\begin_layout LyX-Code
- 1.
- the first file contains the pattern you wish to scan for; I'll
-\end_layout
-
-\begin_layout LyX-Code
- call this file pat_file in what follows (but any name is ok)
-\end_layout
-
-\begin_layout LyX-Code
- 2.
- the second file contains a set of sequences to scan.
- These
-\end_layout
-
-\begin_layout LyX-Code
- should be in "fasta format".
- Just look at the contents of
-\end_layout
-
-\begin_layout LyX-Code
- test_dna_input to see examples of this format.
- Basically,
-\end_layout
-
-\begin_layout LyX-Code
- each sequence begins with a line of the form
-\end_layout
-
-\begin_layout LyX-Code
- >sequence_id
-\end_layout
-
-\begin_layout LyX-Code
- and is followed by one or more lines containing the sequence.
-\end_layout
-
-\begin_layout LyX-Code
- Once these files have been created, you just use
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches pat_file < input_file
-\end_layout
-
-\begin_layout LyX-Code
- to scan all of the input sequences for the given pattern.
- As an
-\end_layout
-
-\begin_layout LyX-Code
- example, suppose that pat_file contains a single line of the form
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...7 3...8 ~p1
-\end_layout
-
-\begin_layout LyX-Code
- Then,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- should produce two "hits".
- When I run this on my machine, I get
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[6,27]
-\end_layout
-
-\begin_layout LyX-Code
- cguaacc ggttaacc gguuacg
-\end_layout
-
-\begin_layout LyX-Code
- >tst2:[6,27]
-\end_layout
-
-\begin_layout LyX-Code
- CGUAACC GGTTAACC GGUUACG
-\end_layout
-
-\begin_layout LyX-Code
- clone%
-\end_layout
-
-\begin_layout LyX-Code
-Simple Patterns Built by Matching Ranges and Reverse Complements
-\end_layout
-
-\begin_layout LyX-Code
- Let me first explain this simple pattern:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...7 3...8 ~p1
-\end_layout
-
-\begin_layout LyX-Code
- The pattern consists of three "pattern units" separated by spaces.
-\end_layout
-
-\begin_layout LyX-Code
- The first pattern unit is
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...7
-\end_layout
-
-\begin_layout LyX-Code
- which means "match 4 to 7 characters and call them p1".
- The
-\end_layout
-
-\begin_layout LyX-Code
- second pattern unit is
-\end_layout
-
-\begin_layout LyX-Code
- 3...8
-\end_layout
-
-\begin_layout LyX-Code
- which means "then match 3 to 8 characters".
- The last pattern unit
-\end_layout
-
-\begin_layout LyX-Code
- is
-\end_layout
-
-\begin_layout LyX-Code
- ~p1
-\end_layout
-
-\begin_layout LyX-Code
- which means "match the reverse complement of p1".
- The first
-\end_layout
-
-\begin_layout LyX-Code
- reported hit is shown as
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[6,27]
-\end_layout
-
-\begin_layout LyX-Code
- cguaacc ggttaacc gguuacg
-\end_layout
-
-\begin_layout LyX-Code
- which states that characters 6 through 27 of sequence tst1 were
-\end_layout
-
-\begin_layout LyX-Code
- matched.
- "cguaac" matched the first pattern unit, "ggttaacc" the
-\end_layout
-
-\begin_layout LyX-Code
- second, and "gguuacg" the third.
- This is an example of a common
-\end_layout
-
-\begin_layout LyX-Code
- type of pattern used to search for sections of DNA or RNA that
-\end_layout
-
-\begin_layout LyX-Code
- would fold into a hairpin loop.
-\end_layout
-
-\begin_layout LyX-Code
-Searching Both Strands
-\end_layout
-
-\begin_layout LyX-Code
- Now for a short aside: scan_for_matches only searched the
-\end_layout
-
-\begin_layout LyX-Code
- sequences in the input file; it did not search the opposite
-\end_layout
-
-\begin_layout LyX-Code
- strand.
- With a pattern of the sort we just used, there is not
-\end_layout
-
-\begin_layout LyX-Code
- need o search the opposite strand.
- However, it is normally the
-\end_layout
-
-\begin_layout LyX-Code
- case that you will wish to search both the sequence and the
-\end_layout
-
-\begin_layout LyX-Code
- opposite strand (i.e., the reverse complement of the sequence).
-\end_layout
-
-\begin_layout LyX-Code
- To do that, you would just use the "-c" command line.
- For example,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches -c pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- Hits on the opposite strand will show a beginning location greater
-\end_layout
-
-\begin_layout LyX-Code
- than te end location of the match.
-\end_layout
-
-\begin_layout LyX-Code
-Defining Pairing Rules and Allowing Mismatches, Insertions, and Deletions
-\end_layout
-
-\begin_layout LyX-Code
- Let us stop now and ask "What additional features would one need to
-\end_layout
-
-\begin_layout LyX-Code
- really find the kinds of loop structures that characterize tRNAs,
-\end_layout
-
-\begin_layout LyX-Code
- rRNAs, and so forth?" I can immediately think of two:
-\end_layout
-
-\begin_layout LyX-Code
- a) you will need to be able to allow non-standard pairings
-\end_layout
-
-\begin_layout LyX-Code
- (those other than G-C and A-U), and
-\end_layout
-
-\begin_layout LyX-Code
- b) you will need to be able to tolerate some number of
-\end_layout
-
-\begin_layout LyX-Code
- mismatches and bulges.
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- Let me first show you how to handle non-standard "rules for
-\end_layout
-
-\begin_layout LyX-Code
- pairing in reverse complements".
- Consider the following pattern,
-\end_layout
-
-\begin_layout LyX-Code
- which I show as two line (you may use as many lines as you like in
-\end_layout
-
-\begin_layout LyX-Code
- forming a pattern, although you can only break a pattern at points
-\end_layout
-
-\begin_layout LyX-Code
- where space would be legal):
-\end_layout
-
-\begin_layout LyX-Code
- r1={au,ua,gc,cg,gu,ug,ga,ag}
-\end_layout
-
-\begin_layout LyX-Code
- p1=2...3 0...4 p2=2...5 1...5 r1~p2 0...4 ~p1
-\end_layout
-
-\begin_layout LyX-Code
- The first "pattern unit" does not actually match anything; rather,
-\end_layout
-
-\begin_layout LyX-Code
- it defines a "pairing rule" in which standard pairings are
-\end_layout
-
-\begin_layout LyX-Code
- allowed, as well as G-A and A-G (in case you wondered, Us and Ts
-\end_layout
-
-\begin_layout LyX-Code
- and upper and lower case can be used interchangably; for example
-\end_layout
-
-\begin_layout LyX-Code
- r1={AT,UA,gc,cg} could be used to define the "standard rule" for
-\end_layout
-
-\begin_layout LyX-Code
- pairings).
- The second line consists of six pattern units which
-\end_layout
-
-\begin_layout LyX-Code
- may be interpreted as follows:
-\end_layout
-
-\begin_layout LyX-Code
- p1=2...3 match 2 or 3 characters (call it p1)
-\end_layout
-
-\begin_layout LyX-Code
- 0...4 match 0 to 4 characters
-\end_layout
-
-\begin_layout LyX-Code
- p2=2...5 match 2 to 5 characters (call it p2)
-\end_layout
-
-\begin_layout LyX-Code
- 1...5 match 1 to 5 characters
-\end_layout
-
-\begin_layout LyX-Code
- r1~p2 match the reverse complement of p2,
-\end_layout
-
-\begin_layout LyX-Code
- allowing G-A and A-G pairs
-\end_layout
-
-\begin_layout LyX-Code
- 0...4 match 0 to 4 characters
-\end_layout
-
-\begin_layout LyX-Code
- ~p1 match the reverse complement of p1
-\end_layout
-
-\begin_layout LyX-Code
- allowing only G-C, C-G, A-T, and T-A pairs
-\end_layout
-
-\begin_layout LyX-Code
- Thus, r1~p2 means "match the reverse complement of p2 using rule r1".
-\end_layout
-
-\begin_layout LyX-Code
- Now let us consider the issue of tolerating mismatches and bulges.
-\end_layout
-
-\begin_layout LyX-Code
- You may add a "qualifier" to the pattern unit that gives the
-\end_layout
-
-\begin_layout LyX-Code
- tolerable number of "mismatches, deletions, and insertions".
-\end_layout
-
-\begin_layout LyX-Code
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- p1=10...10 3...8 ~p1[1,2,1]
-\end_layout
-
-\begin_layout LyX-Code
- means that the third pattern unit must match 10 characters,
-\end_layout
-
-\begin_layout LyX-Code
- allowing one "mismatch" (a pairing other than G-C, C-G, A-T, or
-\end_layout
-
-\begin_layout LyX-Code
- T-A), two deletions (a deletion is a character that occurs in p1,
-\end_layout
-
-\begin_layout LyX-Code
- but has been "deleted" from the string matched by ~p1), and one
-\end_layout
-
-\begin_layout LyX-Code
- insertion (an "insertion" is a character that occurs in the string
-\end_layout
-
-\begin_layout LyX-Code
- matched by ~p1, but not for which no corresponding character
-\end_layout
-
-\begin_layout LyX-Code
- occurs in p1).
- In this case, the pattern would match
-\end_layout
-
-\begin_layout LyX-Code
- ACGTACGTAC GGGGGGGG GCGTTACCT
-\end_layout
-
-\begin_layout LyX-Code
- which is, you must admit, a fairly weak loop.
- It is common to
-\end_layout
-
-\begin_layout LyX-Code
- allow mismatches, but you will find yourself using insertions and
-\end_layout
-
-\begin_layout LyX-Code
- deletions much more rarely.
- In any event, you should note that
-\end_layout
-
-\begin_layout LyX-Code
- allowing mismatches, insertions, and deletions does force the
-\end_layout
-
-\begin_layout LyX-Code
- program to try many additional possible pairings, so it does slow
-\end_layout
-
-\begin_layout LyX-Code
- things down a bit.
-\end_layout
-
-\begin_layout LyX-Code
-How Patterns Are Matched
-\end_layout
-
-\begin_layout LyX-Code
- Now is as good a time as any to discuss the basic flow of control
-\end_layout
-
-\begin_layout LyX-Code
- when matching patterns.
- Recall that a "pattern" is a sequence of
-\end_layout
-
-\begin_layout LyX-Code
- "pattern units".
- Suppose that the pattern units were
-\end_layout
-
-\begin_layout LyX-Code
- u1 u2 u3 u4 ...
- un
-\end_layout
-
-\begin_layout LyX-Code
- The scan of a sequence S begins by setting the current position
-\end_layout
-
-\begin_layout LyX-Code
- to 1.
- Then, an attempt is made to match u1 starting at the
-\end_layout
-
-\begin_layout LyX-Code
- current position.
- Each attempt to match a pattern unit can
-\end_layout
-
-\begin_layout LyX-Code
- succeed or fail.
- If it succeeds, then an attempt is made to match
-\end_layout
-
-\begin_layout LyX-Code
- the next unit.
- If it fails, then an attempt is made to find an
-\end_layout
-
-\begin_layout LyX-Code
- alternative match for the immediately preceding pattern unit.
- If
-\end_layout
-
-\begin_layout LyX-Code
- this succeeds, then we proceed forward again to the next unit.
- If
-\end_layout
-
-\begin_layout LyX-Code
- it fails we go back to the preceding unit.
- This process is called
-\end_layout
-
-\begin_layout LyX-Code
- "backtracking".
- If there are no previous units, then the current
-\end_layout
-
-\begin_layout LyX-Code
- position is incremented by one, and everything starts again.
- This
-\end_layout
-
-\begin_layout LyX-Code
- proceeds until either the current position goes past the end of
-\end_layout
-
-\begin_layout LyX-Code
- the sequence or all of the pattern units succeed.
- On success,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches reports the "hit", the current position is set
-\end_layout
-
-\begin_layout LyX-Code
- just past the hit, and an attempt is made to find another hit.
-\end_layout
-
-\begin_layout LyX-Code
- If you wish to limit the scan to simply finding a maximum of, say,
-\end_layout
-
-\begin_layout LyX-Code
- 10 hits, you can use the -n option (-n 10 would set the limit to
-\end_layout
-
-\begin_layout LyX-Code
- 10 reported hits).
- For example,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches -c -n 1 pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- would search for just the first hit (and would stop searching the
-\end_layout
-
-\begin_layout LyX-Code
- current sequences or any that follow in the input file).
-\end_layout
-
-\begin_layout LyX-Code
-Searching for repeats:
-\end_layout
-
-\begin_layout LyX-Code
- In the last section, I discussed almost all of the details
-\end_layout
-
-\begin_layout LyX-Code
- required to allow you to look for repeats.
- Consider the following
-\end_layout
-
-\begin_layout LyX-Code
- set of patterns:
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...6 3...8 p1 (find exact 6 character repeat separated
-\end_layout
-
-\begin_layout LyX-Code
- by to 8 characters)
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...6 3..8 p1[1,0,0] (allow one mismatch)
-\end_layout
-
-\begin_layout LyX-Code
- p1=3...3 p1[1,0,0] p1[1,0,0] p1[1,0,0]
-\end_layout
-
-\begin_layout LyX-Code
- (match 12 characters that are the remains
-\end_layout
-
-\begin_layout LyX-Code
- of a 3-character sequence occurring 4 times)
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...8 0...3 p2=6...8 p1 0...3 p2
-\end_layout
-
-\begin_layout LyX-Code
- (This would match things like
-\end_layout
-
-\begin_layout LyX-Code
- ATCT G TCTTT ATCT TG TCTTT
-\end_layout
-
-\begin_layout LyX-Code
- )
-\end_layout
-
-\begin_layout LyX-Code
-Searching for particular sequences:
-\end_layout
-
-\begin_layout LyX-Code
- Occasionally, one wishes to match a specific, known sequence.
-\end_layout
-
-\begin_layout LyX-Code
- In such a case, you can just give the sequence (along with an
-\end_layout
-
-\begin_layout LyX-Code
- optional statement of the allowable mismatches, insertions, and
-\end_layout
-
-\begin_layout LyX-Code
- deletions).
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...8 GAGA ~p1 (match a hairpin with GAGA as the loop)
-\end_layout
-
-\begin_layout LyX-Code
- RRRRYYYY (match 4 purines followed by 4 pyrimidines)
-\end_layout
-
-\begin_layout LyX-Code
- TATAA[1,0,0] (match TATAA, allowing 1 mismatch)
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-Matches against a "weight matrix":
-\end_layout
-
-\begin_layout LyX-Code
- I will conclude my examples of the types of pattern units
-\end_layout
-
-\begin_layout LyX-Code
- available for matching against nucleotide sequences by discussing a
-\end_layout
-
-\begin_layout LyX-Code
- crude implemetation of matching using a "weight matrix".
- While I
-\end_layout
-
-\begin_layout LyX-Code
- am less than overwhelmed with the syntax that I chose, I think that
-\end_layout
-
-\begin_layout LyX-Code
- the reader should be aware that I was thinking of generating
-\end_layout
-
-\begin_layout LyX-Code
- patterns containing such pattern units automatically from
-\end_layout
-
-\begin_layout LyX-Code
- alignments (and did not really plan on typing such things in by
-\end_layout
-
-\begin_layout LyX-Code
- hand very often).
- Anyway, suppose that you wanted to match a
-\end_layout
-
-\begin_layout LyX-Code
- sequence of eight characters.
- The "consensus" of these eight
-\end_layout
-
-\begin_layout LyX-Code
- characters is GRCACCGS, but the actual "frequencies of occurrence"
-\end_layout
-
-\begin_layout LyX-Code
- are given in the matrix below.
- Thus, the first character is an A
-\end_layout
-
-\begin_layout LyX-Code
- 16% the time and a G 84% of the time.
- The second is an A 57% of
-\end_layout
-
-\begin_layout LyX-Code
- the time, a C 10% of the time, a G 29% of the time, and a T 4% of
-\end_layout
-
-\begin_layout LyX-Code
- the time.
-
-\end_layout
-
-\begin_layout LyX-Code
- C1 C2 C3 C4 C5 C6 C7 C8
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- A 16 57 0 95 0 18 0 0
-\end_layout
-
-\begin_layout LyX-Code
- C 0 10 80 0 100 60 0 50
-\end_layout
-
-\begin_layout LyX-Code
- G 84 29 0 0 0 20 100 50
-\end_layout
-
-\begin_layout LyX-Code
- T 0 4 20 5 0 2 0 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- One could use the following pattern unit to search for inexact
-\end_layout
-
-\begin_layout LyX-Code
- matches related to such a "weight matrix":
-\end_layout
-
-\begin_layout LyX-Code
- {(16,0,84,0),(57,10,29,4),(0,80,0,20),(95,0,0,5),
-\end_layout
-
-\begin_layout LyX-Code
- (0,100,0,0),(18,60,20,2),(0,0,100,0),(0,50,50,0)} > 450
-\end_layout
-
-\begin_layout LyX-Code
- This pattern unit will attempt to match exactly eight characters.
-\end_layout
-
-\begin_layout LyX-Code
- For each character in the sequence, the entry in the corresponding
-\end_layout
-
-\begin_layout LyX-Code
- tuple is added to an accumulated sum.
- If the sum is greater than
-\end_layout
-
-\begin_layout LyX-Code
- 450, the match succeeds; else it fails.
-\end_layout
-
-\begin_layout LyX-Code
- Recently, this feature was upgraded to allow ranges.
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- 600 > {(16,0,84,0),(57,10,29,4),(0,80,0,20),(95,0,0,5),
-\end_layout
-
-\begin_layout LyX-Code
- (0,100,0,0),(18,60,20,2),(0,0,100,0),(0,50,50,0)} > 450
-\end_layout
-
-\begin_layout LyX-Code
- will work, as well.
-\end_layout
-
-\begin_layout LyX-Code
-Allowing Alternatives:
-\end_layout
-
-\begin_layout LyX-Code
- Very occasionally, you may wish to allow alternative pattern units
-\end_layout
-
-\begin_layout LyX-Code
- (i.e., "match either A or B").
- You can do this using something
-\end_layout
-
-\begin_layout LyX-Code
- like
-\end_layout
-
-\begin_layout LyX-Code
- ( GAGA | GCGCA)
-\end_layout
-
-\begin_layout LyX-Code
- which says "match either GAGA or GCGCA".
- You may take
-\end_layout
-
-\begin_layout LyX-Code
- alternatives of a list of pattern units, for example
-\end_layout
-
-\begin_layout LyX-Code
- (p1=3...3 3...8 ~p1 | p1=5...5 4...4 ~p1 GGG)
-\end_layout
-
-\begin_layout LyX-Code
- would match one of two sequences of pattern units.
- There is one
-\end_layout
-
-\begin_layout LyX-Code
- clumsy aspect of the syntax: to match a list of alternatives, you
-\end_layout
-
-\begin_layout LyX-Code
- need to fully the request.
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- (GAGA | (GCGCA | TTCGA))
-\end_layout
-
-\begin_layout LyX-Code
- would be needed to try the three alternatives.
-\end_layout
-
-\begin_layout LyX-Code
-One Minor Extension
-\end_layout
-
-\begin_layout LyX-Code
- Sometimes a pattern will contain a sequence of distinct ranges,
-\end_layout
-
-\begin_layout LyX-Code
- and you might wish to limit the sum of the lengths of the matched
-\end_layout
-
-\begin_layout LyX-Code
- subsequences.
- For example, suppose that you basically wanted to
-\end_layout
-
-\begin_layout LyX-Code
- match something like
-\end_layout
-
-\begin_layout LyX-Code
- ARRYYTT p1=0...5 GCA[1,0,0] p2=1...6 ~p1 4...8 ~p2 p3=4...10 CCT
-\end_layout
-
-\begin_layout LyX-Code
- but that the sum of the lengths of p1, p2, and p3 must not exceed
-\end_layout
-
-\begin_layout LyX-Code
- eight characters.
- To do this, you could add
-\end_layout
-
-\begin_layout LyX-Code
- length(p1+p2+p3) < 9
-\end_layout
-
-\begin_layout LyX-Code
- as the last pattern unit.
- It will just succeed or fail (but does
-\end_layout
-
-\begin_layout LyX-Code
- not actually match any characters in the sequence).
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-Matching Protein Sequences
-\end_layout
-
-\begin_layout LyX-Code
- Suppose that the input file contains protein sequences.
- In this
-\end_layout
-
-\begin_layout LyX-Code
- case, you must invoke scan_for_matches with the "-p" option.
- You
-\end_layout
-
-\begin_layout LyX-Code
- cannot use aspects of the language that relate directly to
-\end_layout
-
-\begin_layout LyX-Code
- nucleotide sequences (e.g., the -c command line option or pattern
-\end_layout
-
-\begin_layout LyX-Code
- constructs referring to the reverse complement of a previously
-\end_layout
-
-\begin_layout LyX-Code
- matched unit).
-
-\end_layout
-
-\begin_layout LyX-Code
- You also have two additional constructs that allow you to match
-\end_layout
-
-\begin_layout LyX-Code
- either "one of a set of amino acids" or "any amino acid other than
-\end_layout
-
-\begin_layout LyX-Code
- those a given set".
- For example,
-\end_layout
-
-\begin_layout LyX-Code
- p1=0...4 any(HQD) 1...3 notany(HK) p1
-\end_layout
-
-\begin_layout LyX-Code
- would successfully match a string like
-\end_layout
-
-\begin_layout LyX-Code
- YWV D AA C YWV
-\end_layout
-
-\begin_layout LyX-Code
-Using the show_hits Utility
-\end_layout
-
-\begin_layout LyX-Code
- When viewing a large set of complex matches, you might find it
-\end_layout
-
-\begin_layout LyX-Code
- convenient to post-process the scan_for_matches output to get a
-\end_layout
-
-\begin_layout LyX-Code
- more readable version.
- We provide a simple post-processor called
-\end_layout
-
-\begin_layout LyX-Code
- "show_hits".
- To see its effect, just pipe the output of a
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches into show_hits:
-\end_layout
-
-\begin_layout LyX-Code
- Normal Output:
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches -c pat_file < tmp
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[1,28]
-\end_layout
-
-\begin_layout LyX-Code
- gtacguaacc ggttaac cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[28,1]
-\end_layout
-
-\begin_layout LyX-Code
- gtacgtaacc ggttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- >tst2:[2,31]
-\end_layout
-
-\begin_layout LyX-Code
- CGTACGUAAC C GGTTAACC GGUUACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- >tst2:[31,2]
-\end_layout
-
-\begin_layout LyX-Code
- CGTACGTAAC C GGTTAACC GGTTACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- >tst3:[3,32]
-\end_layout
-
-\begin_layout LyX-Code
- gtacguaacc g gttaactt cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- >tst3:[32,3]
-\end_layout
-
-\begin_layout LyX-Code
- gtacgtaacc g aagttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- Piped Through show_hits:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches -c pat_file < tmp | show_hits
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[1,28]: gtacguaacc ggttaac cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[28,1]: gtacgtaacc ggttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[2,31]: CGTACGUAAC C GGTTAACC GGUUACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[31,2]: CGTACGTAAC C GGTTAACC GGTTACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[3,32]: gtacguaacc g gttaactt cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[32,3]: gtacgtaacc g aagttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- clone%
-\end_layout
-
-\begin_layout LyX-Code
- Optionally, you can specify which of the "fields" in the matches
-\end_layout
-
-\begin_layout LyX-Code
- you wish to sort on, and show_hits will sort them.
- The field
-\end_layout
-
-\begin_layout LyX-Code
- numbers start with 0.
- So, you might get something like
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches -c pat_file < tmp | show_hits 2 1
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[2,31]: CGTACGUAAC C GGTTAACC GGUUACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[31,2]: CGTACGTAAC C GGTTAACC GGTTACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[32,3]: gtacgtaacc g aagttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[1,28]: gtacguaacc ggttaac cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[28,1]: gtacgtaacc ggttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[3,32]: gtacguaacc g gttaactt cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- clone%
-\end_layout
-
-\begin_layout LyX-Code
- In this case, the hits have been sorted on fields 2 and 1 (that is,
-\end_layout
-
-\begin_layout LyX-Code
- the third and second matched subfields).
-\end_layout
-
-\begin_layout LyX-Code
- show_hits is just one possible little post-processor, and you
-\end_layout
-
-\begin_layout LyX-Code
- might well wish to write a customized one for yourself.
-\end_layout
-
-\begin_layout LyX-Code
-Reducing the Cost of a Search
-\end_layout
-
-\begin_layout LyX-Code
- The scan_for_matches utility uses a fairly simple search, and may
-\end_layout
-
-\begin_layout LyX-Code
- consume large amounts of CPU time for complex patterns.
- Someday,
-\end_layout
-
-\begin_layout LyX-Code
- I may decide to optimize the code.
- However, until then, let me
-\end_layout
-
-\begin_layout LyX-Code
- mention one useful technique.
-
-\end_layout
-
-\begin_layout LyX-Code
- When you have a complex pattern that includes a number of varying
-\end_layout
-
-\begin_layout LyX-Code
- ranges, imprecise matches, and so forth, it is useful to
-\end_layout
-
-\begin_layout LyX-Code
- "pipeline" matches.
- That is, form a simpler pattern that can be
-\end_layout
-
-\begin_layout LyX-Code
- used to scan through a large database extracting sections that
-\end_layout
-
-\begin_layout LyX-Code
- might be matched by the more complex pattern.
- Let me illustrate
-\end_layout
-
-\begin_layout LyX-Code
- with a short example.
- Suppose that you really wished to match the
-\end_layout
-
-\begin_layout LyX-Code
- pattern
-\end_layout
-
-\begin_layout LyX-Code
- p1=3...5 0...8 ~p1[1,1,0] p2=6...7 3...6 AGC 3...5 RYGC ~p2[1,0,0]
-\end_layout
-
-\begin_layout LyX-Code
- In this case, the pattern units AGC 3...5 RYGC can be used to rapidly
-\end_layout
-
-\begin_layout LyX-Code
- constrain the overall search.
- You can preprocess the overall
-\end_layout
-
-\begin_layout LyX-Code
- database using the pattern:
-\end_layout
-
-\begin_layout LyX-Code
- 31...31 AGC 3...5 RYGC 7...7
-\end_layout
-
-\begin_layout LyX-Code
- Put the complex pattern in pat_file1 and the simpler pattern in
-\end_layout
-
-\begin_layout LyX-Code
- pat_file2.
- Then use,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches -c pat_file2 < nucleotide_database |
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches pat_file1
-\end_layout
-
-\begin_layout LyX-Code
- The output will show things like
-\end_layout
-
-\begin_layout LyX-Code
- >seqid:[232,280][2,47]
-\end_layout
-
-\begin_layout LyX-Code
- matches pieces
-\end_layout
-
-\begin_layout LyX-Code
- Then, the actual section of the sequence that was matched can be
-\end_layout
-
-\begin_layout LyX-Code
- easily computed as [233,278] (remember, the positions start from
-\end_layout
-
-\begin_layout LyX-Code
- 1, not 0).
-\end_layout
-
-\begin_layout LyX-Code
- Let me finally add, you should do a few short experiments to see
-\end_layout
-
-\begin_layout LyX-Code
- whether or not such pipelining actually improves performance -- it
-\end_layout
-
-\begin_layout LyX-Code
- is not always obvious where the time is going, and I have
-\end_layout
-
-\begin_layout LyX-Code
- sometimes found that the added complexity of pipelining actually
-\end_layout
-
-\begin_layout LyX-Code
- slowed things up.
- It gets its best improvements when there are
-\end_layout
-
-\begin_layout LyX-Code
- exact matches of more than just a few characters that can be
-\end_layout
-
-\begin_layout LyX-Code
- rapidly used to eliminate large sections of the database.
-\end_layout
-
-\begin_layout LyX-Code
-=============
-\end_layout
-
-\begin_layout LyX-Code
-Additions:
-\end_layout
-
-\begin_layout LyX-Code
-Feb 9, 1995: the pattern units ^ and $ now work as in normal regular
-\end_layout
-
-\begin_layout LyX-Code
- expressions.
- That is
-\end_layout
-
-\begin_layout LyX-Code
- TTF $
-\end_layout
-
-\begin_layout LyX-Code
- matches only TTF at the end of the string and
-\end_layout
-
-\begin_layout LyX-Code
- ^ TTF
-\end_layout
-
-\begin_layout LyX-Code
- matches only an initial TTF
-\end_layout
-
-\begin_layout LyX-Code
- The pattern unit
-\end_layout
-
-\begin_layout LyX-Code
- <p1
-\end_layout
-
-\begin_layout LyX-Code
- matches the reverse of the string named p1.
- That is,
-\end_layout
-
-\begin_layout LyX-Code
- if p1 matched GCAT, then <p1 would match TACG.
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...6 <p1
-\end_layout
-
-\begin_layout LyX-Code
- matches a real palindrome (not the biologically common
-\end_layout
-
-\begin_layout LyX-Code
- meaning of "reverse complement")
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\end_body
-\end_document
+++ /dev/null
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
-\begin_document
-\begin_header
-\textclass scrartcl
-\begin_preamble
-\usepackage[colorlinks=true, urlcolor=blue, linkcolor=black]{hyperref}
-\end_preamble
-\language english
-\inputencoding auto
-\font_roman default
-\font_sans default
-\font_typewriter default
-\font_default_family default
-\font_sc false
-\font_osf false
-\font_sf_scale 100
-\font_tt_scale 100
-\graphics default
-\paperfontsize default
-\spacing single
-\papersize default
-\use_geometry false
-\use_amsmath 1
-\use_esint 1
-\cite_engine basic
-\use_bibtopic false
-\paperorientation portrait
-\secnumdepth 3
-\tocdepth 3
-\paragraph_separation skip
-\defskip medskip
-\quotes_language english
-\papercolumns 1
-\papersides 1
-\paperpagestyle default
-\tracking_changes false
-\output_changes false
-\author ""
-\author ""
-\end_header
-
-\begin_body
-
-\begin_layout Title
-Biopieces Cookbook
-\end_layout
-
-\begin_layout Author
-Martin Asser Hansen
-\end_layout
-
-\begin_layout Publishers
-John Mattick Group
-\newline
-Institute for Molecular Bioscience
-\newline
-University of Queensland
-\newline
-Aust
-ralia
-\newline
-E-mail: mail@maasha.dk
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
-
-\backslash
-thispagestyle{empty}
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-
-\newpage
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset LatexCommand tableofcontents
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset FloatList figure
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-
-\newpage
-
-\end_layout
-
-\begin_layout Section
-Introduction
-\end_layout
-
-\begin_layout Standard
-Biopieces is a collection of simple tools that can be linked together (piped
- as we shall call it) in a very flexible manner to perform both simple and
- complex tasks.
- The fundamental idea is that biopieces work on a data stream that will
- only terminate at the end of an analysis and that this data stream can
- be passed through several different biopieces, each performing one specific
- task.
- The advantage of this approach is that a user can perform simple and complex
- tasks without having to write advanced code.
- Moreover, since the data format used to pass data between biopieces is
- text based, biopieces can be written by different developers in their favorite
- programming language --- and still the biopieces will be able to work together.
-\end_layout
-
-\begin_layout Standard
-In the most simple form bioools can be piped together on the command line
- like this (using the pipe character '|'):
-\end_layout
-
-\begin_layout LyX-Code
-read_data | calculate_something | write_result
-\end_layout
-
-\begin_layout Standard
-However, a more comprehensive analysis could be composed:
-\end_layout
-
-\begin_layout LyX-Code
-read_data | select_entries | convert_entries | search_database
-\end_layout
-
-\begin_layout LyX-Code
-evaluate_results | plot_diagram | plot_another_diagram |
-\end_layout
-
-\begin_layout LyX-Code
-load_to_database
-\end_layout
-
-\begin_layout Standard
-The data stream that is piped through the biopieces consists of records
- of key/value pairs in the same way a hash does in order to keep as simple
- a structure as possible.
- An example record can be seen below:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-REC_TYPE: PATSCAN
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-MATCH: AGATCAAGTG
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-S_BEG: 7
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-S_END: 16
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-ALIGN_LEN: 9
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-S_ID: piR-t6
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-STRAND: +
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-PATTERN: AGATCAAGTG
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
----
-\end_layout
-
-\begin_layout Standard
-The '
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-' denotes the delimiter of the records, and each key is a word followed
- by a ':' and a white-space and then the value.
- By convention the biopieces only uses upper case keys (a list of used keys
- can be seen in Appendix\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sec:Keys"
-
-\end_inset
-
-).
- Since the records basically are hash structures this mean that the order
- of the keys in the stream is unordered, and in the above example it is
- pure coincidence that HIT_BEG is displayed before HIT_END, however, when
- the order of the keys is importent, the biopieces will automagically see
- to that.
-\end_layout
-
-\begin_layout Standard
-All of the biopieces are able to read and write a data stream to and from
- file as long as the records are in the biopieces format.
- This means that if you are undertaking a lengthy analysis where one of
- the steps is time consuming, you may save the stream after this step, and
- subsequently start one or more analysis from that last step
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-It is a goal that the biopieces at some point will be able to dump the data
- stream to file in case one of the tools fail critically.
-\end_layout
-
-\end_inset
-
-.
- If you are running a lengthy analysis it is highly recommended that you
- create a small test sample of the data and run that through the pipeline
- --- and once you are satisfied with the result proceed with the full data
- set (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-select-a-few-records"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Standard
-All of the biopieces can be supplied with long arguments prefixed with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
- switches or single character arguments prefixed with - switches that can
- be grouped together (e.g.
- -xok).
- In this cookbook only the long switches are used to emphasize what these
- switches do.
-\end_layout
-
-\begin_layout Section
-Setup
-\end_layout
-
-\begin_layout Standard
-In order to get the biopieces to work, you need to add environment settings
- to include the code binaries, scripts, and modules that constitute the
- biopieces package.
- Assuming that you are using bash, add the following to your '~/.bashrc'
- file using your favorite editor.
- After the changes has been saved you need to either run 'source ~/.bashrc'
- or relogin.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-if [ -f "/home/m.hansen/maasha/conf/bashrc" ]; then
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- source "/home/m.hansen/maasha/conf/bashrc"
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-fi
-\end_layout
-
-\begin_layout Section
-Getting Started
-\end_layout
-
-\begin_layout Standard
-The biopiece
-\series bold
-list_biopieces
-\series default
- lists all the biopieces along with a description:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-list_biopieces
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-align_seq Align sequences in stream using Muscle.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-analyze_seq Analysis the residue composition of each sequence
- in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-analyze_vals Determine type, count, min, max, sum and mean for
- values in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-blast_seq BLAST sequences in stream against a specified database.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-blat_seq BLAT sequences in stream against a specified genome.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-complement_seq Complement sequences in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_records Count the number of records in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_seq Count sequences in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_vals Count the number of times values of given keys exists
- in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-create_blast_db Create a BLAST database from sequences in stream for
- use with BLAST.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-...
-\end_layout
-
-\begin_layout Standard
-To list the biopieces for writing different formats, you can use unix's
- grep like this:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-list_biopieces | grep write
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_align Write aligned sequences in pretty alignment format.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_bed Write records from stream as BED lines.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_blast Write BLAST records from stream in BLAST tabular format
- (-m8 and 9).
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_fasta Write sequences in FASTA format.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_psl Write records from stream in PSL format.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_tab Write records from stream as tab separated table.
-\end_layout
-
-\begin_layout Standard
-In order to find out how a specific biopiece works, you just type the program
- name without any arguments and press return and the usage of the biopiece
- will be displayed.
- E.g.
-
-\series bold
-read_fasta
-\series default
- <return>:
-\end_layout
-
-\begin_layout Standard
-\begin_inset Box Frameless
-position "t"
-hor_pos "c"
-has_inner_box 1
-inner_pos "t"
-use_parbox 0
-width "100col%"
-special "none"
-height "1in"
-height_special "totalheight"
-status open
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Program name: read_fasta
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Contact: mail@maasha.dk
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Date: August 2007
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/
-gpl.html)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Description: Read FASTA entries.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Usage: read_fasta [options] -i <FASTA file(s)>
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Options:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-i <file(s)> | --data_in=<file(s)>] - Comma separated list of files
- to read.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-n <int> | --num=<int>] - Limit number of records to read.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-I <file> | --stream_in=<file>] - Read input stream from file
- - Default=STDIN
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-O <file> | --stream_out=<file>] - Write output stream to file
- - Default=STDOUT
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Examples:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i test.fna - Read FASTA entries from file.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i test1.fna,test2,fna - Read FASTA entries from files.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i '*.fna' - Read FASTA entries from files.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i test.fna -n 10 - Read first 10 FASTA entries from
- file.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Section
-The Data Stream
-\end_layout
-
-\begin_layout Subsection
-How to read the data stream from file?
-\begin_inset LatexCommand label
-name "sub:How-to-read-stream"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-You want to read a data stream that you previously have saved to file in
- biopieces format.
- This can be done implicetly or explicitly.
- The implicit way uses the 'stdout' stream of the Unix terminal:
-\end_layout
-
-\begin_layout LyX-Code
-cat | <biopiece>
-\end_layout
-
-\begin_layout Standard
-cat is the Unix command that reads a file and output the result to 'stdout'
- --- which in this case is piped to any biopiece represented by the <biopiece>.
- It is also possible to read the data stream using '<' to direct the 'stdout'
- stream into the biopiece like this:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> < <file>
-\end_layout
-
-\begin_layout Standard
-However, that will not work if you pipe more biopieces together.
- Then it is much safer to read the stream from a file explicitly like this:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --stream_in=<file>
-\end_layout
-
-\begin_layout Standard
-Here the filename <file> is explicetly given to the biopiece <biopiece>
- with the switch
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_in.
- This switch works with all biopieces.
- It is also possible to read in data from multiple sources by repeating
- the explicit read step:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --stream_in=<file1> | <biopiece> --stream_in=<file2>
-\end_layout
-
-\begin_layout Subsection
-How to write the data stream to file?
-\begin_inset LatexCommand label
-name "sub:How-to-write-stream"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-In order to save the output stream from a biopiece to file, so you can read
- in the stream again at a later time, you can do one of two things:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> > <file>
-\end_layout
-
-\begin_layout Standard
-All, the biopieces write the data stream to 'stdout' by default which can
- be written to a file by redirecting 'stdout' to file using '>' , however,
- if one of the biopieces for writing other formats is used then the both
- the biopieces records as well as the result output will go to 'stdout'
- in a mixture causing havock! To avoid this you must use the switch
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_out that explictly tells the biopiece to write the output stream
- to file:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --stream_out=<file>
-\end_layout
-
-\begin_layout Standard
-The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_out switch works with all biopieces.
-\end_layout
-
-\begin_layout Subsection
-How to terminate the data stream?
-\end_layout
-
-\begin_layout Standard
-The data stream is never stops unless the user want to save the stream or
- by supplying the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch that will terminate the stream:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --no_stream
-\end_layout
-
-\begin_layout Standard
-The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch only works with those biopieces where it makes sense that
- the user might want to terminale the data stream,
-\emph on
-i.e
-\emph default
-.
- after an analysis step where the user wants to output the result, but not
- the data stream.
-\end_layout
-
-\begin_layout Subsection
-How to write my results to file?
-\begin_inset LatexCommand label
-name "sub:How-to-write-result"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Saving the result of an analysis to file can be done implicitly or explicitly.
- The implicit way:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --no_stream > <file>
-\end_layout
-
-\begin_layout Standard
-If you use '>' to redirect 'stdout' to file then it is important to use
- the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch to avoid writing a mix of biopieces records and result
- to the same file causing havock.
- The safe way is to use the
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out switch which explicetly tells the biopiece to write the result
- to a given file:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --result_out=<file>
-\end_layout
-
-\begin_layout Standard
-Using the above method will not terminate the stream, so it is possible
- to pipe that into another biopiece generating different results:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece1> --result_out=<file1> | <biopiece2> --result_out=<file2>
-\end_layout
-
-\begin_layout Standard
-And still the data stream will continue unless terminated with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --result_out=<file> --no_stream
-\end_layout
-
-\begin_layout Standard
-Or written to file using implicitly or explicity
-\begin_inset LatexCommand eqref
-reference "sub:How-to-write-result"
-
-\end_inset
-
-.
- The explicit way:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --result_out=<file1> --stream_out=<file2>
-\end_layout
-
-\begin_layout Subsection
-How to read data from multiple sources?
-\end_layout
-
-\begin_layout Standard
-To read multiple data sources, with the same type or different type of data
- do:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece1> --data_in=<file1> | <biopiece2> --data_in=<file2>
-\end_layout
-
-\begin_layout Standard
-where type is the data type a specific biopiece reads.
-\end_layout
-
-\begin_layout Section
-Reading input
-\end_layout
-
-\begin_layout Subsection
-How to read biopieces input?
-\end_layout
-
-\begin_layout Standard
-See
-\begin_inset LatexCommand eqref
-reference "sub:How-to-read-stream"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Subsection
-How to read in data?
-\end_layout
-
-\begin_layout Standard
-Data in different formats can be read with the appropriate biopiece for
- that format.
- The biopieces are typicalled named 'read_<data type>' such as
-\series bold
-read_fasta
-\series default
-,
-\series bold
-read_bed
-\series default
-,
-\series bold
-read_tab
-\series default
-, etc., and all behave in a similar manner.
- Data can be read by supplying the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-data_in switch and a file name to the file containing the data:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --data_in=<file>
-\end_layout
-
-\begin_layout Standard
-It is also possible to read in a saved biopieces stream (see
-\begin_inset LatexCommand ref
-reference "sub:How-to-read-stream"
-
-\end_inset
-
-) as well as reading data in one go:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --stream_in=<file1> --data_in=<file2>
-\end_layout
-
-\begin_layout Standard
-If you want to read data from several files you can do this:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --data_in=<file1> | <biopiece> --data_in=<file2>
-\end_layout
-
-\begin_layout Standard
-If you have several data files you can read in all explicitly with a comma
- separated list:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --data_in=file1,file2,file3
-\end_layout
-
-\begin_layout Standard
-And it is also possible to use file globbing
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-using the short option will only work if you quote the argument -i '*.fna'
-\end_layout
-
-\end_inset
-
-:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --data_in=*.fna
-\end_layout
-
-\begin_layout Standard
-Or in a combination:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece> --data_in=file1,/dir/*.fna
-\end_layout
-
-\begin_layout Standard
-Finally, it is possible to read in data in different formats using the appropria
-te biopiece for each format:
-\end_layout
-
-\begin_layout LyX-Code
-<biopiece1> --data_in=<file1> | <biopiece2> --data_in=<file2> ...
-\end_layout
-
-\begin_layout Subsection
-How to read FASTA input?
-\end_layout
-
-\begin_layout Standard
-Sequences in FASTA format can be read explicitly using
-\series bold
-read_fasta
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file>
-\end_layout
-
-\begin_layout Subsection
-How to read alignment input?
-\end_layout
-
-\begin_layout Standard
-If your alignment if FASTA formatted then you can
-\series bold
-read_align
-\series default
-.
- It is also possible to use
-\series bold
-read_fasta
-\series default
- since the data is FASTA formatted, however, with
-\series bold
-read_fasta
-\series default
- the key ALIGN will be omitted.
- The ALIGN key is used to determine which sequences belong to what alignment
- which is required for
-\series bold
-write_align
-\series default
-.
-\end_layout
-
-\begin_layout LyX-Code
-read_align --data_in=<file>
-\end_layout
-
-\begin_layout Subsection
-How to read tabular input?
-\begin_inset LatexCommand label
-name "sub:How-to-read-table"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Tabular input can be read with
-\series bold
-read_tab
-\series default
- which will read in all rows and chosen columns (separated by a given delimter)
- from a table in text format.
-\end_layout
-
-\begin_layout Standard
-The table below:
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Tabular
-<lyxtabular version="3" rows="4" columns="3">
-<features>
-<column alignment="left" valignment="top" width="0">
-<column alignment="left" valignment="top" width="0">
-<column alignment="left" valignment="top" width="0">
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Human
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-ATACGTCAG
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-23524
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Dog
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-AGCATGAC
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-2442
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Mouse
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-GACTG
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-234
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Cat
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-AAATGCA
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-2342
-\end_layout
-
-\end_inset
-</cell>
-</row>
-</lyxtabular>
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Can be read using the command:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file>
-\end_layout
-
-\begin_layout Standard
-Which will result in four records, one for each row, where the keys V0,
- V1, V2 are the default keys for the organism, sequence, and count, respectively.
- It is possible to select a subset of colums to read by using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-cols switch which takes a comma separated list of columns numbers (first
- column is designated 0) as argument.
- So to read in only the sequence and the count so that the count comes before
- the sequence do:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file> --cols=2,1
-\end_layout
-
-\begin_layout Standard
-It is also possible to name the columns with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys switch:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file> --cols=2,1 --keys=COUNT,SEQ
-\end_layout
-
-\begin_layout Subsection
-How to read BED input?
-\end_layout
-
-\begin_layout Standard
-The BED (Browser Extensible Data
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://genome.ucsc.edu/FAQ/FAQformat"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-) format is a tabular format for data pertaining to one of the Eukaryotic
- genomes in the UCSC genome brower
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://genome.ucsc.edu/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-.
- The BED format consists of up to 12 columns, where the first three are
- mandatory CHR, CHR_BEG, and CHR_END.
- The mandatory columns and any of the optional columns can all be read in
- easily with the
-\series bold
-read_bed
-\series default
- biopiece.
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<file>
-\end_layout
-
-\begin_layout Standard
-It is also possible to read the BED file with
-\series bold
-read_tab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-read-table"
-
-\end_inset
-
-), however, that will be more cumbersome because you need to specify the
- keys:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file> --keys=CHR,CHR_BEG,CHR_END ...
-\end_layout
-
-\begin_layout Subsection
-How to read PSL input?
-\end_layout
-
-\begin_layout Standard
-The PSL format is the output from BLAT and contains 21 mandatory fields
- that can be read with
-\series bold
-read_psl
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-read_psl --data_in=<file>
-\end_layout
-
-\begin_layout Section
-Writing output
-\end_layout
-
-\begin_layout Standard
-All result output can be written explicitly to file using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out switch which all result generating biopieces have.
- It is also possible to write the result to file implicetly by directing
- 'stdout' to file using '>', however, that requires the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream swich to prevent a mixture of data stream and results in the file.
- The explicit (and safe) way:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | <biopiece> --result_out=<file>
-\end_layout
-
-\begin_layout Standard
-The implicit way:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | <biopiece> --no_stream > <file>
-\end_layout
-
-\begin_layout Subsection
-How to write biopieces output?
-\end_layout
-
-\begin_layout Standard
-See
-\begin_inset LatexCommand eqref
-reference "sub:How-to-write-stream"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Subsection
-How to write FASTA output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-fasta"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-FASTA output can be written with
-\series bold
-write_fasta
-\series default
-.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_fasta --result_out=<file>
-\end_layout
-
-\begin_layout Standard
-It is also possible to wrap the sequences to a given width using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-wrap switch allthough wrapping of sequence is generally an evil thing:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_fasta --no_stream --wrap=80
-\end_layout
-
-\begin_layout Subsection
-How to write alignment output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-alignment"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Pretty alignments with ruler
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-'.' for every 10 residues, ':' for every 50, and '|' for every 100
-\end_layout
-
-\end_inset
-
- and consensus sequence
-\begin_inset Note Note
-status collapsed
-
-\begin_layout Standard
-which reminds me to make that an option.
-\end_layout
-
-\end_inset
-
- can be created with
-\series bold
-write_align
-\series default
-, what also have the optional
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-wrap switch to break the alignment into blocks of a given width:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_align --result_out=<file> --wrap=80
-\end_layout
-
-\begin_layout Standard
-If the number of sequnces in the alignment is 2 then a pairwise alignment
- will be output otherwise a multiple alignment.
- And if the sequence type, determined automagically, is protein, then residues
- and symbols (+,\InsetSpace ~
-:,\InsetSpace ~
-.) will be used to show consensus according to the Blosum62
- matrix.
-\end_layout
-
-\begin_layout Subsection
-How to write tabular output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-tab"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Outputting the data stream as a table can be done with
-\series bold
-write_tab
-\series default
-, which will write generate one row per record with the values as columns.
- If you supply the optional
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-comment switch, when the first row in the table will be a 'comment' line
- prefixed with a '#':
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --comment
-\end_layout
-
-\begin_layout Standard
-You can also change the delimiter from the default (tab) to
-\emph on
-e.g.
-
-\emph default
- ',':
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --delimit=','
-\end_layout
-
-\begin_layout Standard
-If you want the values output in a specific order you have to supply a comma
- separated list using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys switch that will print only those keys in that order:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --keys=SEQ_NAME,COUNT
-\end_layout
-
-\begin_layout Standard
-Alternatively, if you have some keys that you don't want in the tabular
- output, use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_keys switch.
- So to print all keys except SEQ and SEQ_TYPE do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --no_keys=SEQ,SEQ_TYPE
-\end_layout
-
-\begin_layout Standard
-Finally, if you have a stream containing a mix of different records types,
-
-\emph on
-e.g.
-
-\emph default
- records with sequences and records with matches, then you can use
-\series bold
-write_tab
-\series default
- to output all the records in tabluar format, however, the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-comment,
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys, and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_keys switches will only respond to records of the first type encountered.
- The reason is that outputting mixed records is probably not what you want
- anyway, and you should remove all the unwanted records from the stream
- before outputting the table:
-\series bold
-grab
-\series default
- is your friend (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-grab"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to write a BED output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-BED"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Data in BED format can be output if the records contain the mandatory keys
- CHR, CHR_BEG, and CHR_END using
-\series bold
-write_bed
-\series default
-.
- If the optional keys are also present, they will be output as well:
-\end_layout
-
-\begin_layout LyX-Code
-write_bed --result_out=<file>
-\end_layout
-
-\begin_layout Subsection
-How to write PSL output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-PSL"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Data in PSL format can be output using
-\series bold
-write_psl:
-\end_layout
-
-\begin_layout LyX-Code
-write_psl --result_out=<file>
-\end_layout
-
-\begin_layout Section
-Manipulating Records
-\end_layout
-
-\begin_layout Subsection
-How to select a few records?
-\begin_inset LatexCommand label
-name "sub:How-to-select-a-few-records"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-To quickly get an overview of your data you can limit the data stream to
- show a few records.
- This also very useful to test the pipeline with a few records if you are
- setting up a complex analysis using several biopieces.
- That way you can inspect that all goes well before analyzing and waiting
- for the full data set.
- All of the read_<type> biopieces have the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num switch which will take a number as argument and only that number of
- records will be read.
- So to read in the first 10 FASTA entries from a file:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna --num=10
-\end_layout
-
-\begin_layout Standard
-Another way of doing this is to use
-\series bold
-head_records
-\series default
- will limit the stream to show the first 10 records (default):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | head_records
-\end_layout
-
-\begin_layout Standard
-Using
-\series bold
-head_records
-\series default
- directly after one of the read_<type> biopieces will be a lot slower than
- using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num switch with the read_<type> biopieces, however,
-\series bold
-head_records
-\series default
- can also be used to limit the output from all the other biopieces.
- It is also possible to give
-\series bold
-head_records
-\series default
- a number of records to show using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num switch.
- So to display the first 100 records do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | head_records --num=100
-\end_layout
-
-\begin_layout Subsection
-How to select random records?
-\begin_inset LatexCommand label
-name "sub:How-to-select-random-records"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-If you want to inspect a number of random records from the stream this can
- be done with the
-\series bold
-random_records
-\series default
- biopiece.
- So if you have 1 mio records in the stream and you want to select 1000
- random records do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | random_records --num=1000
-\end_layout
-
-\begin_layout Subsection
-How to count all records in the data stream?
-\end_layout
-
-\begin_layout Standard
-To count all the records in the data stream use
-\series bold
-count_records
-\series default
-, which adds one record (which is not included in the count) to the data
- stream.
- So to count the number of sequences in a FASTA file you can do this:
-\end_layout
-
-\begin_layout LyX-Code
-cat test.fna | read_fasta | count_records --no_stream
-\end_layout
-
-\begin_layout Standard
-Which will write the last record containing the count to 'stdout':
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_records: 630
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
----
-\end_layout
-
-\begin_layout Standard
-It is also possible to write the count to file using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out switch.
-\end_layout
-
-\begin_layout Subsection
-How to get the length of record values?
-\begin_inset LatexCommand label
-name "sub:How-to-get-value_length"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Use the
-\series bold
-length_vals
-\series default
- biopiece to get the length of each value for a comma separated list of
- keys:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | length_vals --keys=HIT,PATTERN
-\end_layout
-
-\begin_layout Subsection
-How to grab specific records?
-\begin_inset LatexCommand label
-name "sub:How-to-grab"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The biopiece
-\series bold
-grab
-\series default
- is related to the Unix grep and locates records based on matching keys
- and/or values using either a pattern, a Perl regex, or a numerical evaluation.
- To easily
-\series bold
-grab
-\series default
- all records in the stream that has any mentioning of the pattern 'human'
- just pipe the data stream through
-\series bold
-grab
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human
-\end_layout
-
-\begin_layout Standard
-This will search for the pattern 'human' in all keys and all values.
- The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern switch takes a comma separated list of patterns, so in order to
- match multiple patterns do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human,mouse
-\end_layout
-
-\begin_layout Standard
-It is also possible to use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in switch instead of
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern.
-
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in is used to read a file with one pattern per line:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern_in=patterns.txt
-\end_layout
-
-\begin_layout Standard
-If you want the opposite result --- to find all records that does not match
- the patterns, add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-invert switch, which not only works with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern switch, but also with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-regex and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-eval:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human --invert
-\end_layout
-
-\begin_layout Standard
-If you want to search the record keys only,
-\emph on
-e.g.
-
-\emph default
- to find all records containing the key SEQ you can add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys_only switch.
- This will prevent matching of SEQ in any record value, and in fact SEQ
- is a not uncommon peptide sequence you could get an unwanted record.
- Also, this will give an increase in speed since only the keys are searched:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=SEQ --keys_only
-\end_layout
-
-\begin_layout Standard
-However, if you are interested in finding the peptide sequence SEQ and not
- the SEQ key, just add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-vals_only switch instead:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=SEQ --vals_only
-\end_layout
-
-\begin_layout Standard
-Also, if you want to grab for certain key/value pairs you can supply a comma
- separated list of keys whos values will then be searched using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys switch.
- This is handy if your records contain large genomic sequences and you dont
- want to search the entire sequence for
-\emph on
-e.g.
-
-\emph default
- the organism name --- it is much faster to tell
-\series bold
-grab
-\series default
- which keys to search the value for:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human --keys=SEQ_NAME
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout Standard
-It is also possible to invoke flexible matching using regex (regular expressions
-) instead of simple pattern matching.
- In
-\series bold
-grab
-\series default
- the regex engine is Perl based and allows use of different type of wild
- cards, alternatives,
-\emph on
-etc
-\emph default
-
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://perldoc.perl.org/perlreref.html"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-.
- If you want to
-\series bold
-grab
-\series default
- records withs the sequence ATCG or GCTA you can do this:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --regex='ATCG|GCTA'
-\end_layout
-
-\begin_layout Standard
-Or if you want to find sequences beginning with ATCG:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --regex='^ATCG'
-\end_layout
-
-\begin_layout Standard
-You can also use
-\series bold
-grab
-\series default
- to locate records that fulfill a numerical property using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-eval switch witch takes an expression in three parts.
- The first part is the key that holds the value we want to evaluate, the
- second part holds one the six operators:
-\end_layout
-
-\begin_layout Enumerate
-Greater than: >
-\end_layout
-
-\begin_layout Enumerate
-Greater than or equal to: >=
-\end_layout
-
-\begin_layout Enumerate
-Less than: <
-\end_layout
-
-\begin_layout Enumerate
-Less than or equal to: <=
-\end_layout
-
-\begin_layout Enumerate
-Equal to: =
-\end_layout
-
-\begin_layout Enumerate
-Not equal to: !=
-\end_layout
-
-\begin_layout Enumerate
-String wise equal to: eq
-\end_layout
-
-\begin_layout Enumerate
-String wise not equal to: ne
-\end_layout
-
-\begin_layout Standard
-And finally comes the number used in the evaluation.
- So to
-\series bold
-grab
-\series default
- all records with a sequence length greater than 30:
-\end_layout
-
-\begin_layout LyX-Code
-...
- length_seq | grab --eval='SEQ_LEN > 30'
-\end_layout
-
-\begin_layout Standard
-If you want to locate all records containing the pattern 'human' and where
- the sequence length is greater that 30, you do this by running the stream
- through
-\series bold
-grab
-\series default
- twice:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern='human' | length_seq | grab --eval='SEQ_LEN > 30'
-\end_layout
-
-\begin_layout Standard
-Finally, it is possible to do fast matching of expressions from a file using
- the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-exact switch.
- Each of these expressions has to be matched exactly over the entrie length,
- which if useful if you have a file with accession numbers, that you want
- to locate in the stream:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --exact acc_no.txt | ...
-\end_layout
-
-\begin_layout Standard
-Using
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-exact is much faster than using
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in, because with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-exact the expression has to be complete matches, where
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in looks for subpatterns.
-\end_layout
-
-\begin_layout Standard
-NB! To get the best speed performance, use the most restrictive
-\series bold
-grab
-\series default
- first.
-\end_layout
-
-\begin_layout Subsection
-How to remove keys from records?
-\end_layout
-
-\begin_layout Standard
-To remove one or more specific keys from all records in the data stream
- use
-\series bold
-remove_keys
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | remove_keys --keys=SEQ,SEQ_NAME
-\end_layout
-
-\begin_layout Standard
-In the above example SEQ and SEQ_NAME will be removed from all records if
- they exists in these.
- If all keys are removed from a record, then the record will be removed.
-\end_layout
-
-\begin_layout Subsection
-How to rename keys in records?
-\end_layout
-
-\begin_layout Standard
-Sometimes you want to rename a record key,
-\emph on
-e.g.
-
-\emph default
- if you have read in a two column table with sequence name and sequence
- in each column (see
-\begin_inset LatexCommand ref
-reference "sub:How-to-read-table"
-
-\end_inset
-
-) without specifying the key names, then the sequence name will be called
- V0 and the sequence V1 as default in the
-\series bold
-read_tab
-\series default
- biopiece.
- To rename the V0 and V1 keys we need to run the stream through
-\series bold
-rename_keys
-\series default
- twice (one for each key to rename):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | rename_keys --keys=V0,SEQ_NAME | rename_keys --keys=V1,SEQ
-\end_layout
-
-\begin_layout Standard
-The first instance of
-\series bold
-rename_keys
-\series default
- replaces all the V0 keys with SEQ_NAME, and the second instance of
-\series bold
-rename_keys
-\series default
- replaces all the V1 keys with SEQ.
-
-\emph on
-Et viola
-\emph default
- the data can now be used in the biopieces that requires these keys.
-\end_layout
-
-\begin_layout Section
-Manipulating Sequences
-\end_layout
-
-\begin_layout Subsection
-How to get sequence lengths?
-\end_layout
-
-\begin_layout Standard
-The length for sequences in records can be determined with
-\series bold
-length_seq
-\series default
-, which adds the key SEQ_LEN to each record with the sequence length as
- the value.
- It also generates an extra record that is emitted last with the key TOTAL_SEQ_L
-EN showing the total length of all the sequences.
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_seq
-\end_layout
-
-\begin_layout Standard
-It is also possible to determine the sequence length using the generic tool
-
-\series bold
-length_vals
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-get-value_length"
-
-\end_inset
-
-, which determines the length of the values for a given list of keys:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_vals --keys=SEQ
-\end_layout
-
-\begin_layout Standard
-To obtain the total length of all sequences use
-\series bold
-sum_vals
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_vals --keys=SEQ
-\end_layout
-
-\begin_layout LyX-Code
-| sum_vals --keys=SEQ_LEN
-\end_layout
-
-\begin_layout Standard
-The biopiece
-\series bold
-analyze_seq
-\series default
- will also determine the length of each sequence (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-analyze"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to analyze sequence composition?
-\begin_inset LatexCommand label
-name "sub:How-to-analyze"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-If you want to find out the sequence type, composition, length, as well
- as GC content, indel content and proportions of soft and hard masked sequence,
- then use
-\series bold
-analyze_seq
-\series default
-.
- This handy biopiece will determine all these things per sequence from which
- it is easy to get an overview using the
-\series bold
-write_tab
-\series default
- biopiece to output a table (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-tab"
-
-\end_inset
-
-).
- So in order to determine the sequence composition of a FASTA file with
- just one entry containing the sequence 'ATCG' we just read the data with
-
-\series bold
-read_fasta
-\series default
- and run the output through
-\series bold
-analyze_seq
-\series default
- which will add the analysis to the record like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq ...
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:D: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-MIX_INDEX: 0.55
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:W: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:G: 16
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SOFT_MASK%: 63.75
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:B: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:V: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-HARD_MASK%: 0.00
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:H: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:S: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:N: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:.: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-GC%: 35.00
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:A: 8
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:Y: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:M: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:T: 44
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SEQ_TYPE: DNA
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:K: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:~: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SEQ: TTTCAGTTTGGGACGGAGTAAGGCCTTCCtttttttttttttttttttttttttttttgagaccgagtcttgctc
-tgtcg
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SEQ_LEN:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-80 RES:R: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:C: 12
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:-: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:U: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
----
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout Standard
-Now to make a table of how may As, Ts, Cs, and Gs you can add the following:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | analyze_seq | write_tab --keys=RES:A,RES:T,RES:C,RES:G
-\end_layout
-
-\begin_layout Standard
-Or if you want to see the proportions of hard and soft masked sequence:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | analyse_seq | write_tab --keys=HARD_MASK%,SOFT_MASK%
-\end_layout
-
-\begin_layout Standard
-If you have a stack of sequences in one file and you want to determine the
- mean GC content you can do it using the
-\series bold
-mean_vals
-\series default
- biopiece:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq | mean_vals --keys=GC%
-\end_layout
-
-\begin_layout Standard
-Or if you want the total count of Ns you can use
-\series bold
-sum_vals
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq | sum_vals --keys=RES:N
-\end_layout
-
-\begin_layout Standard
-The MIX_INDEX key is calculated as the count of the most common residue
- over the sequence length, and can be used as a cut-off for removing sequence
- tags consisting of mostly one nucleotide:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq | grab --eval='MIX_INDEX<0.85'
-\end_layout
-
-\begin_layout Subsection
-How to extract subsequences?
-\begin_inset LatexCommand label
-name "sub:How-to-extract"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-In order to extract a subsequence from a longer sequence use the biopiece
- extract_seq, which will replace the sequence in the record with the subsequence
- (this behaviour should probably be modified to be dependant of a
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-replace or a
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_replace switch
-\begin_inset Note Note
-status collapsed
-
-\begin_layout Standard
-also in split_seq
-\end_layout
-
-\end_inset
-
-).
- So to extract the first 20 residues from all sequences do (first residue
- is designated 1):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | extract_seq --beg=1 --len=20
-\end_layout
-
-\begin_layout Standard
-You can also specify a begin and end coordinate set:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | extract_seq --beg=20 --end=40
-\end_layout
-
-\begin_layout Standard
-If you want the subsequences from position 20 to the sequence end do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | extract_seq --beg=20
-\end_layout
-
-\begin_layout Standard
-If you want to extract subsequences a given distance from the sequence end
- you can do this by reversing the sequence with the biopiece
-\series bold
-reverse_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-reverse-seq"
-
-\end_inset
-
-, followed by
-\series bold
-extract_seq
-\series default
- to get the subsequence, and then
-\series bold
-reverse_seq
-\series default
- again to get the subsequence back in the original orientation:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | reverse_seq
-\end_layout
-
-\begin_layout LyX-Code
-| extract_seq --beg=10 --len=10 | reverse_seq
-\end_layout
-
-\begin_layout Subsection
-How to get genomic sequence?
-\begin_inset LatexCommand label
-name "sub:How-to-get-genomic-sequence"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The biopiece
-\series bold
-get_genomic_seq
-\series default
- can extract subsequences for a given genome specified with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-genome switch explicitly using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-beg and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-end/
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-len switches:
-\end_layout
-
-\begin_layout LyX-Code
-get_genome_seq --genome=<genome> --beg=1 --len=100
-\end_layout
-
-\begin_layout Standard
-Alternatively,
-\series bold
-get_genome_seq
-\series default
- can be used to append the corresponding sequence to BED, PSL, and BLAST
- records:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<BED file> | get_genome_seq --genome=<genome>
-\end_layout
-
-\begin_layout Standard
-It is also possible to include flaking sequence using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-flank switch.
- So to include 50 nucleotides upstream and 50 nucleotides downstream for
- each BED entry do:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<BED file> | get_genome_seq --genome=<genome> --flank=50
-\end_layout
-
-\begin_layout Subsection
-How to upper-case sequences?
-\end_layout
-
-\begin_layout Standard
-Sequences can be shifted from lower case to upper case using
-\series bold
-uppercase_seq
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | uppercase_seq
-\end_layout
-
-\begin_layout Subsection
-How to reverse sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-reverse-seq"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The order of residues in a sequence can be reversed using reverse_seq:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | reverse_seq
-\end_layout
-
-\begin_layout Standard
-Note that in order to reverse/complement a sequence you also need the
-\series bold
-complement_seq
-\series default
- biopiece (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-complement"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to complement sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-complement"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-DNA and RNA sequences can be complemented with
-\series bold
-complement_seq
-\series default
-, which automagically determines the sequence type:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | complement_seq
-\end_layout
-
-\begin_layout Standard
-Note that in order to reverse/complement a sequence you also need the
-\series bold
-reverse_seq
-\series default
- biopiece (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-reverse-seq"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to remove indels from sequnces?
-\end_layout
-
-\begin_layout Standard
-Indels can be removed from sequences with the
-\series bold
-remove_indels
-\series default
- biopiece.
- This is useful if you have aligned some sequences (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-align"
-
-\end_inset
-
-) and extracted (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-extract"
-
-\end_inset
-
-) a block of subsequences from the alignment and you want to use these sequence
- in a search where you need to remove the indels first.
- '-', '~', and '.' are considered indels:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | remove_indels
-\end_layout
-
-\begin_layout Subsection
-How to shuffle sequences?
-\end_layout
-
-\begin_layout Standard
-All residues in sequences in the stream can be shuffled to random positions
- using the
-\series bold
-shuffle_seq
-\series default
- biopiece:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | shuffle_seq
-\end_layout
-
-\begin_layout Subsection
-How to split sequences into overlapping subsequences?
-\end_layout
-
-\begin_layout Standard
-Sequences can be slit into overlapping subsequences with the
-\series bold
-split_seq
-\series default
- biopiece.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | split_seq --word_size=20 --uniq
-\end_layout
-
-\begin_layout Subsection
-How to determine the oligo frequency?
-\end_layout
-
-\begin_layout Standard
-In order to determine if any oligo usage is over represented in one or more
- sequences you can determine the frequency of oligos of a given size with
-
-\series bold
-oligo_freq
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | oligo_freq --word_size=4
-\end_layout
-
-\begin_layout Standard
-And if you have more than one sequence and want to accumulate the frequences
- you need the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-all switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | oligo_freq --word_size=4 --all
-\end_layout
-
-\begin_layout Standard
-To get a meaningful result you need to write the resulting frequencies as
- a table with
-\series bold
-write_tab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-tab"
-
-\end_inset
-
-), but first it is important to
-\series bold
-grab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-grab"
-
-\end_inset
-
-) the records with the frequencies to avoid full length sequences in the
- table:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | oligo_freq --word_size=4 --all | grab --pattern=OLIGO --keys_only
-\end_layout
-
-\begin_layout LyX-Code
-| write_tab --no_stream
-\end_layout
-
-\begin_layout Standard
-And the resulting frequency table can be sorted with Unix sort (man sort).
-\end_layout
-
-\begin_layout Subsection
-How to search for sequences in genomes?
-\end_layout
-
-\begin_layout Standard
-See the following biopiece:
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-patscan_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-patscan"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-blat_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAT"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-blast_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAST"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-vmatch_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-Vmatch"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to search sequences for a pattern?
-\begin_inset LatexCommand label
-name "sub:How-to-use-patscan"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-It is possible to search sequences in the data stream for patterns using
- the
-\series bold
-patscan_seq
-\series default
- biopiece which utilizes the powerful scan_for_matches engine.
- Consult the documentation for scan_for_matches in order to learn how to
- define patterns (the documentation is included in Appendix\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sec:scan_for_matches-README"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Standard
-To search all sequences for a simple pattern consisting of the sequence
- ATCGATCG allowing for 3 mismatches, 2 insertions and 1 deletion:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | patscan_seq --pattern='ATCGATCG[3,2,1]'
-\end_layout
-
-\begin_layout Standard
-The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern switch takes a comma seperated list of patterns, so if you want
- to search for more that one pattern do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern='ATCGATCG[3,2,1],GCTAGCTA[3,2,1]'
-\end_layout
-
-\begin_layout Standard
-It is also possible to have a list of different patterns to search for in
- a file with one pattern per line.
- In order to get
-\series bold
-patscan_seq
-\series default
- to read these patterns use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern_in=<file>
-\end_layout
-
-\begin_layout Standard
-To also scan the complementary strand in nucleotide sequences (
-\series bold
-patscan_seq
-\series default
- automagically determines the sequence type) you need to add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-comp switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern=<pattern> --comp
-\end_layout
-
-\begin_layout Standard
-It is also possible to use
-\series bold
-patscan_seq
-\series default
- to output those records that does not contain a certain pattern by using
- the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-invert switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern=<pattern> --invert
-\end_layout
-
-\begin_layout Standard
-Finally,
-\series bold
-patscan_seq
-\series default
- can also scan for patterns in a given genome sequence, instead of sequences
- in the stream, using the
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-genome switch:
-\end_layout
-
-\begin_layout LyX-Code
-patscan --pattern=<pattern> --genome=<genome>
-\end_layout
-
-\begin_layout Subsection
-How to use BLAT for sequence search?
-\begin_inset LatexCommand label
-name "sub:How-to-use-BLAT"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Sequences in the data stream can be matched against supported genomes using
-
-\series bold
-blat_seq
-\series default
- which is a biopiece using BLAT as the name might suggest.
- Currently only Mouse and Human genomes are available and it is not possible
- to use OOC files since there is still a need for a local repository for
- genome files.
- Otherwise it is just:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | blat_seq --genome=<genome>
-\end_layout
-
-\begin_layout Standard
-The search results can then be written to file with
-\series bold
-write_psl
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-PSL"
-
-\end_inset
-
-) or
-\series bold
-write_bed
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-BED"
-
-\end_inset
-
-) allthough with
-\series bold
-write_bed
-\series default
- some information will be lost).
- It is also possible to plot chromosome distribution of the search results
- using
-\series bold
-plot_chrdist
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-plot-chrdist"
-
-\end_inset
-
-) or the distribution of the match lengths using
-\series bold
-plot_lendist
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-plot-lendist"
-
-\end_inset
-
-) or a karyogram with the hits using
-\series bold
-plot_karyogram
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-plot-karyogram"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to use BLAST for sequence search?
-\begin_inset LatexCommand label
-name "sub:How-to-use-BLAST"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Two biopieces exist for blasting sequences:
-\series bold
-create_blast_db
-\series default
- is used to create the BLAST database required for BLAST which is queried
- using the biopiece
-\series bold
-blast_seq
-\series default
-.
- So in order to create a BLAST database from sequences in the data stream
- you simple run:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_blast_db --database=my_database --no_stream
-\end_layout
-
-\begin_layout Standard
-The type of sequence to use for the database is automagically determined
- by
-\series bold
-create_blast_db
-\series default
-, but don't have a mixture of peptide and nucleic acids sequences in the
- stream.
- The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-database switch takes a path as argument, but will default to 'blastdb_<time_sta
-mp> if not set.
-\end_layout
-
-\begin_layout Standard
-The resulting database can now be queried with sequences in another data
- stream using
-\series bold
-blast_seq
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | blast_seq --database=my_database
-\end_layout
-
-\begin_layout Standard
-Again, the sequence type is determined automagically and the appropriate
- BLAST program is guessed (see below table), however, the program name can
- be overruled with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-program switch.
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Tabular
-<lyxtabular version="3" rows="5" columns="3">
-<features>
-<column alignment="center" valignment="top" width="0">
-<column alignment="center" valignment="top" width="0">
-<column alignment="center" valignment="top" width="0">
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Subject sequence
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Query sequence
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Program guess
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-blastn
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-blastp
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-blastx
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-tblastn
-\end_layout
-
-\end_inset
-</cell>
-</row>
-</lyxtabular>
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Finally, it is also possible to use
-\series bold
-blast_seq
-\series default
- for blasting sequences agains a preformatted genome using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-genome switch instead of the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-database switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | blast_seq --genome=<genome>
-\end_layout
-
-\begin_layout Subsection
-How to use Vmatch for sequence search?
-\begin_inset LatexCommand label
-name "sub:How-to-use-Vmatch"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The powerful suffix array software package Vmatch
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://www.vmatch.de/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
- can be used for exact mapping of sequences against indexed genomes using
- the biopiece
-\series bold
-vmatch_seq
-\series default
-, which will e.g.
- map 700000 ESTs to the human genome locating all 160 mio hits in less than
- an hour.
- Only nucleotide sequences and sequences longer than 11 nucleotides will
- be mapped.
- It is recommended that sequences consisting of mostly one nucleotide type
- are removed.
- This can be done with the
-\series bold
-analyze_seq
-\series default
- biopiece
-\begin_inset LatexCommand eqref
-reference "sub:How-to-analyze"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome>
-\end_layout
-
-\begin_layout Standard
-It is also possible to allow for mismatches using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-hamming_dist switch.
- So to allow for 2 mismatches:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=2
-\end_layout
-
-\begin_layout Standard
-Or to allow for 10% mismathing nucleotides:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=10p
-\end_layout
-
-\begin_layout Standard
-To allow both indels and mismatches use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-edit_dist switch.
- So to allow for one mismatch or one indel:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=1
-\end_layout
-
-\begin_layout Standard
-Or to allow for 5% indels or mismatches:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=5p
-\end_layout
-
-\begin_layout Standard
-Note that using
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-hamming_dist or
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-edit_dist greatly slows down vmatch considerably --- use with care.
-\end_layout
-
-\begin_layout Standard
-The resulting SCORE key can be replaced to hold the number of genome matches
- of a given sequence (multi-mappers) is the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-count switch is given.
-\end_layout
-
-\begin_layout Subsection
-How to find all matches between sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-find-matches"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-All matches between two sequences can be determined with the biopiece
-\series bold
-match_seq
-\series default
-.
- The match finding engine underneath the hood of
-\series bold
-match_seq
-\series default
- is the super fast suffix tree program MUMmer
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://mummer.sourceforge.net/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-, which will locate all forward and reverse matches between huge sequences
- in a matter of minutes (if the repeat count is not too high and if the
- word size used is appropriate).
- Matching two
-\emph on
-Helicobacter pylori
-\emph default
- genomes (1.7Mbp) takes around 10 seconds:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | match_seq --word_size=20 --direction=both
-\end_layout
-
-\begin_layout Standard
-The output from
-\series bold
-match_seq
-\series default
- can be used to generate a dot plot with
-\series bold
-plot_matches
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-generate-dotplot"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to align sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-align"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Sequences in the stream can be aligned with the
-\series bold
-align_seq
-\series default
- biopiece that uses Muscle
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://www.drive5.com/muscle/muscle.html"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
- as aligment engine.
- Currently you cannot change any of the Muscle alignment parameters and
-
-\series bold
-align_seq
-\series default
- will create an alignment based on the defaults (which are really good!):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | align_seq
-\end_layout
-
-\begin_layout Standard
-The aligned output can be written to file in FASTA format using
-\series bold
-write_fasta
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-fasta"
-
-\end_inset
-
-) or in pretty text using
-\series bold
-write_align
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-alignment"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to create a weight matrix?
-\end_layout
-
-\begin_layout Standard
-If you want a weight matrix to show the sequence composition of a stack
- of sequences you can use the biopiece create_weight_matrix:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_weight_matrix
-\end_layout
-
-\begin_layout Standard
-The result can be output in percent using the
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-percent switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_weight_matrix --percent
-\end_layout
-
-\begin_layout Standard
-The weight matrix can be written as tabular output with
-\series bold
-write_tab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-tab"
-
-\end_inset
-
-) after removeing the records containing SEQ with
-\series bold
-grab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-grab"
-
-\end_inset
-
-):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_weight_matrix | grab --invert --keys=SEQ --keys_only
-\end_layout
-
-\begin_layout LyX-Code
-| write_tab --no_stream
-\end_layout
-
-\begin_layout Standard
-The V0 column will hold the residue, while the rest of the columns will
- hold the frequencies for each sequence position.
-\end_layout
-
-\begin_layout Section
-Plotting
-\end_layout
-
-\begin_layout Standard
-There exists several biopieces for plotting.
- Some of these are based on GNUplot
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://www.gnuplot.info/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-, which is an extremely powerful platform to generate all sorts of plots
- and even though GNUplot has quite a steep learning curve, the biopieces
- utilizing GNUplot are simple to use.
- GNUplot is able to output a lot of different formats (called terminals
- in GNUplot), but the biopieces focusses on three formats only:
-\end_layout
-
-\begin_layout Enumerate
-The 'dumb' terminal is default to the GNUplot based biopieces and will output
- a plot in crude ASCII text (Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Dumb-terminal"
-
-\end_inset
-
-).
- This is quite nice for a quick and dirty plot to get an overview of your
- data .
-\end_layout
-
-\begin_layout Enumerate
-The 'post' or 'postscript' terminal output postscript code which is publication
- grade graphics that can be viewed with applications such as Ghostview,
- Photoshop, and Preview.
-\end_layout
-
-\begin_layout Enumerate
-The 'svg' terminal output's scalable vector graphics (SVG) which is a vector
- based format.
- SVG is great because you can edit the resulting plot using Photoshop or
- Inkscape
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-Inkscape is a really handy drawing program that is free and open source.
- Availble at
-\begin_inset LatexCommand htmlurl
-target "http://www.inkscape.org"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
- if you want to add additional labels, captions, arrows, and so on and then
- save the result in different formats, such as postscript without loosing
- resolution.
-\end_layout
-
-\begin_layout Standard
-The biopieces for plotting that are not based on GNUplot only output SVG
- (that may change in the future).
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename lendist_ascii.png
- lyxscale 70
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Dumb-terminal"
-
-\end_inset
-
-Dumb terminal
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-The output of a length distribution plot in the default 'dumb terminal'
- to the terminal window.
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a histogram?
-\begin_inset LatexCommand label
-name "How-to-plot-histogram"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-A generic histogram for a given value can be plotted with the biopiece
-\series bold
-plot_histogram
-\series default
- (Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Histogram"
-
-\end_inset
-
-):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_histogram --key=TISSUE --no_stream
-\end_layout
-
-\begin_layout Standard
-(Figure missing)
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align left
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename histogram.png
- lyxscale 70
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Histogram"
-
-\end_inset
-
-Histogram
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a length distribution?
-\begin_inset LatexCommand label
-name "sub:How-to-plot-lendist"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Plotting of length distributions, weather sequence lengths, patterns lengths,
- hit lengths,
-\emph on
-etc.
-
-\emph default
- is a really handy thing and can be done with the the biopiece
-\series bold
-plot_lendist
-\series default
-.
- If you have a file with FASTA entries and want to plot the length distribution
- you do it like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_seq
-\end_layout
-
-\begin_layout LyX-Code
-| plot_lendist --key=SEQ_LEN --no_stream
-\end_layout
-
-\begin_layout Standard
-The result will be written to the default dumb terminal and will look like
- Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Dumb-terminal"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-If you instead want the result in postscript format you can do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_lendist --key=SEQ_LEN --terminal=post --result_out=file.ps
-\end_layout
-
-\begin_layout Standard
-That will generate the plot and save it to file, but not interrupt the data
- stream which can then be used in further analysis.
- You can also save the plot implicetly using '>', however, it is then important
- to terminate the stream with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_lendist --key=SEQ_LEN --terminal=post --no_stream > file.ps
-\end_layout
-
-\begin_layout Standard
-The resulting plot can be seen in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Length-distribution"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename lendist.ps
- lyxscale 50
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Length-distribution"
-
-\end_inset
-
-Length distribution
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-Length distribution of 630 piRNA like RNAs.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a chromosome distribution?
-\begin_inset LatexCommand label
-name "sub:How-to-plot-chrdist"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-If you have the result of a sequence search against a multi chromosome genome,
- it is very practical to be able to plot the distribution of search hits
- on the different chromosomes.
- This can be done with
-\series bold
-plot_chrdist
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | blat_genome | plot_chrdist --no_stream
-\end_layout
-
-\begin_layout Standard
-The above example will result in a crude plot using the 'dumb' terminal,
- and if you want to mess around with the results from the BLAT search you
- probably want to save the result to file first (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-PSL"
-
-\end_inset
-
-).
- To plot the chromosome distribution from the saved search result you can
- do:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=file.bed | plot_chrdist --terminal=post --result_out=plot.ps
-\end_layout
-
-\begin_layout Standard
-That will result in the output show in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Chromosome-distribution"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename chrdist.ps
- lyxscale 50
- width 12cm
- rotateAngle 90
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Chromosome-distribution"
-
-\end_inset
-
-Chromosome distribution
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to generate a dotplot?
-\begin_inset LatexCommand label
-name "sub:How-to-generate-dotplot"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-A dotplot is a powerful way to get an overview of the size and location
- of sequence insertions, deletions, and duplications between two sequences.
- Generating a dotplot with biopieces is a two step process where you initially
- find all matches between two sequences using the tool
-\series bold
-match_seq
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-find-matches"
-
-\end_inset
-
-) and plot the resulting matches with
-\series bold
-plot_matches
-\series default
-.
- Matching and plotting two
-\emph on
-Helicobacter pylori
-\emph default
- genomes (1.7Mbp) takes around 10 seconds:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | match_seq | plot_matches --terminal=post --result_out=plot.ps
-\end_layout
-
-\begin_layout Standard
-The resulting dotplot is in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Dotplot"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename dotplot.ps
- lyxscale 50
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Dotplot"
-
-\end_inset
-
-Dotplot
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-Forward matches are displayed in green while reverse matches are displayed
- in red.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a sequence logo?
-\end_layout
-
-\begin_layout Standard
-Sequence logos can be generate with
-\series bold
-plot_seqlogo
-\series default
-.
- The sequnce type is determined automagically and an entropy scale of 2
- bits and 4 bits is used for nucleotide and peptide sequences, respectively
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand htmlurl
-target "http://www.ccrnp.ncifcrf.gov/~toms/paper/hawaii/latex/node5.html"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_seqlogo --no_stream --result_out=seqlogo.svg
-\end_layout
-
-\begin_layout Standard
-An example of a sequence logo can be seen in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Sequence-logo"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename seqlogo.png
- lyxscale 50
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Sequence-logo"
-
-\end_inset
-
-Sequence logo
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a karyogram?
-\begin_inset LatexCommand label
-name "sub:How-to-plot-karyogram"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-To plot search hits on genomes use
-\series bold
-plot_karyogram
-\series default
-, which will output a nice karyogram in SVG graphics:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_karyogram --result_out=karyogram.svg
-\end_layout
-
-\begin_layout Standard
-The banding data is taken from the UCSC genome browser database and currently
- only Human and Mouse is supported.
- Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Karyogram"
-
-\end_inset
-
- shows the distribution of piRNA like RNAs matched to the Human genome.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename karyogram.png
- lyxscale 35
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Karyogram"
-
-\end_inset
-
-Karyogram
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-Hits from a search of piRNA like RNAs in the Human genome is displayed as
- short horizontal bars.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Section
-Uploading Results
-\end_layout
-
-\begin_layout Subsection
-How do I display my results in the UCSC Genome Browser?
-\end_layout
-
-\begin_layout Standard
-Results from the list of biopieces below can be uploaded directly to a local
- mirror of the UCSC Genome Browser using the biopiece
-\series bold
-upload_to_ucsc
-\series default
-:
-\end_layout
-
-\begin_layout Itemize
-patscan_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-patscan"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-blat_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAT"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-blast_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAST"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-vmatch_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-Vmatch"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The syntax for uploading data the most simple way requires two mandatory
- switches:
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-database, which is the UCSC database name (such as hg18, mm9, etc.) and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-table which should be the users initials followed by an underscore and a
- short description of the data:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | upload_to_ucsc --database=hg18 --table=mah_snoRNAs
-\end_layout
-
-\begin_layout Standard
-The
-\series bold
-upload_to_ucsc
-\series default
- biopiece modifies the users ~/ucsc/my_tracks.ra file automagically (a backup
- is created with the name ~/ucsc/my_tracks.ra~) with default values that
- can be overridden using the following switches:
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-short_label - Short label for track - Default=database->table
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-long_label - Long label for track - Default=database->table
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-group - Track group name - Default=<user name as defined in env>
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-priority - Track display priority - Default=1
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-color - Track color - Default=147,73,42
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-chunk_size - Chunks for loading - Default=10000000
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-visibility - Track visibility - Default=pack
-\end_layout
-
-\begin_layout Standard
-Also, data in BED or PSL format can be uploaded with
-\series bold
-upload_to_ucsc
-\series default
- as long as these reference to genomes and chromosomes existing in the UCSC
- Genome Browser:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<bed file> | upload_to_ucsc ...
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-read_psl --data_in=<psl file> | upload_to_ucsc ...
-\end_layout
-
-\begin_layout Section
-Power Scripting
-\end_layout
-
-\begin_layout Standard
-It is possible to do commandline scripting of biopiece records using Perl.
- Because a biopiece record essentially is a hash structure, you can pass
- records to
-\series bold
-bioscript
-\series default
- command, which is a wrapper around the Perl executable that allows direct
- manipulations of the records using the power of Perl.
-\end_layout
-
-\begin_layout Standard
-In the below example we replace in all records the value to the CHR key
- with a forthrunning number:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | bioscript 'while($r=get_record(
-\backslash
-*STDIN)){$r->{CHR}=$i++; put_record($r)}'
-\end_layout
-
-\begin_layout Standard
-Something more useful would probably be to create custom FASTA headers.
- E.g.
- if we read in a BED file, lookup the genomic sequence, create a custom
- FASTA header with
-\series bold
-bioscript
-\series default
- and output FASTA entries:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | bioscript 'while($r=get_record(
-\backslash
-*STDIN)){$r->{SEQ_NAME}= //
-\end_layout
-
-\begin_layout LyX-Code
-join("_",$r->{CHR},$r->{CHR_BEG},$r->{CHR_END}); put_record($r)}'
-\end_layout
-
-\begin_layout Standard
-And the output:
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_21567527_21567550
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_693380_693403
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_13859534_13859557
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_9005090_9005113
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_2106825_2106848
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_14649031_14649054
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout Section
-Trouble shooting
-\end_layout
-
-\begin_layout Standard
-Shoot the messenger!
-\end_layout
-
-\begin_layout Section
-\start_of_appendix
-Keys
-\begin_inset LatexCommand label
-name "sec:Keys"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-HIT
-\end_layout
-
-\begin_layout Standard
-HIT_BEG
-\end_layout
-
-\begin_layout Standard
-HIT_END
-\end_layout
-
-\begin_layout Standard
-HIT_LEN
-\end_layout
-
-\begin_layout Standard
-HIT_NAME
-\end_layout
-
-\begin_layout Standard
-PATTERN
-\end_layout
-
-\begin_layout Section
-Switches
-\begin_inset LatexCommand label
-name "sec:Switches"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_in
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_out
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-data_in
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num
-\end_layout
-
-\begin_layout Section
-scan_for_matches README
-\begin_inset LatexCommand label
-name "sec:scan_for_matches-README"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches:
-\end_layout
-
-\begin_layout LyX-Code
- A Program to Scan Nucleotide or Protein Sequences for Matching Patterns
-\end_layout
-
-\begin_layout LyX-Code
- Ross Overbeek
-\end_layout
-
-\begin_layout LyX-Code
- MCS
-\end_layout
-
-\begin_layout LyX-Code
- Argonne National Laboratory
-\end_layout
-
-\begin_layout LyX-Code
- Argonne, IL 60439
-\end_layout
-
-\begin_layout LyX-Code
- USA
-\end_layout
-
-\begin_layout LyX-Code
-Scan_for_matches is a utility that we have written to search for
-\end_layout
-
-\begin_layout LyX-Code
-patterns in DNA and protein sequences.
- I wrote most of the code,
-\end_layout
-
-\begin_layout LyX-Code
-although David Joerg and Morgan Price wrote sections of an
-\end_layout
-
-\begin_layout LyX-Code
-earlier version.
- The whole notion of pattern matching has a rich
-\end_layout
-
-\begin_layout LyX-Code
-history, and we borrowed liberally from many sources.
- However, it is
-\end_layout
-
-\begin_layout LyX-Code
-worth noting that we were strongly influenced by the elegant tools
-\end_layout
-
-\begin_layout LyX-Code
-developed and distributed by David Searls.
- My intent is to make the
-\end_layout
-
-\begin_layout LyX-Code
-existing tool available to anyone in the research community that might
-\end_layout
-
-\begin_layout LyX-Code
-find it useful.
- I will continue to try to fix bugs and make suggested
-\end_layout
-
-\begin_layout LyX-Code
-enhancements, at least until I feel that a superior tool exists.
-\end_layout
-
-\begin_layout LyX-Code
-Hence, I would appreciate it if all bug reports and suggestions are
-\end_layout
-
-\begin_layout LyX-Code
-directed to me at Overbeek@mcs.anl.gov.
-
-\end_layout
-
-\begin_layout LyX-Code
-I will try to log all bug fixes and report them to users that send me
-\end_layout
-
-\begin_layout LyX-Code
-their email addresses.
- I do not require that you give me your name
-\end_layout
-
-\begin_layout LyX-Code
-and address.
- However, if you do give it to me, I will try to notify
-\end_layout
-
-\begin_layout LyX-Code
-you of serious problems as they are discovered.
-\end_layout
-
-\begin_layout LyX-Code
-Getting Started:
-\end_layout
-
-\begin_layout LyX-Code
- The distribution should contain at least the following programs:
-\end_layout
-
-\begin_layout LyX-Code
- README - This document
-\end_layout
-
-\begin_layout LyX-Code
- ggpunit.c - One of the two source files
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches.c - The second source file
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- run_tests - A perl script to test things
-\end_layout
-
-\begin_layout LyX-Code
- show_hits - A handy perl script
-\end_layout
-
-\begin_layout LyX-Code
- test_dna_input - Test sequences for DNA
-\end_layout
-
-\begin_layout LyX-Code
- test_dna_patterns - Test patterns for DNA scan
-\end_layout
-
-\begin_layout LyX-Code
- test_output - Desired output from test
-\end_layout
-
-\begin_layout LyX-Code
- test_prot_input - Test protein sequences
-\end_layout
-
-\begin_layout LyX-Code
- test_prot_patterns - Test patterns for proteins
-\end_layout
-
-\begin_layout LyX-Code
- testit - a perl script used for test
-\end_layout
-
-\begin_layout LyX-Code
- Only the first three files are required.
- The others are useful,
-\end_layout
-
-\begin_layout LyX-Code
- but only if you have Perl installed on your system.
- If you do
-\end_layout
-
-\begin_layout LyX-Code
- have Perl, I suggest that you type
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- which perl
-\end_layout
-
-\begin_layout LyX-Code
- to find out where it installed.
- On my system, I get the following
-\end_layout
-
-\begin_layout LyX-Code
- response:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- clone% which perl
-\end_layout
-
-\begin_layout LyX-Code
- /usr/local/bin/perl
-\end_layout
-
-\begin_layout LyX-Code
- indicating that Perl is installed in /usr/local/bin.
- Anyway, once
-\end_layout
-
-\begin_layout LyX-Code
- you know where it is installed, edit the first line of files
-\end_layout
-
-\begin_layout LyX-Code
- testit
-\end_layout
-
-\begin_layout LyX-Code
- show_hits
-\end_layout
-
-\begin_layout LyX-Code
- replacing /usr/local/bin/perl with the appropriate location.
- I
-\end_layout
-
-\begin_layout LyX-Code
- will assume that you can do this, although it is not critical (it
-\end_layout
-
-\begin_layout LyX-Code
- is needed only to test the installation and to use the "show_hits"
-\end_layout
-
-\begin_layout LyX-Code
- utility).
- Perl is not required to actually install and run
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches.
-
-\end_layout
-
-\begin_layout LyX-Code
- If you do not have Perl, I suggest you get it and install it (it
-\end_layout
-
-\begin_layout LyX-Code
- is a wonderful utility).
- Information about Perl and how to get it
-\end_layout
-
-\begin_layout LyX-Code
- can be found in the book "Programming Perl" by Larry Wall and
-\end_layout
-
-\begin_layout LyX-Code
- Randall L.
- Schwartz, published by O'Reilly & Associates, Inc.
-\end_layout
-
-\begin_layout LyX-Code
- To get started, you will need to compile the program.
- I do this
-\end_layout
-
-\begin_layout LyX-Code
- using
-\end_layout
-
-\begin_layout LyX-Code
- gcc -O -o scan_for_matches ggpunit.c scan_for_matches.c
-\end_layout
-
-\begin_layout LyX-Code
- If you do not use GNU C, use
-\end_layout
-
-\begin_layout LyX-Code
- cc -O -DCC -o scan_for_matches ggpunit.c scan_for_matches.c
-\end_layout
-
-\begin_layout LyX-Code
- which works on my Sun.
-
-\end_layout
-
-\begin_layout LyX-Code
- Once you have compiled scan_for_matches, you can verify that it
-\end_layout
-
-\begin_layout LyX-Code
- works with
-\end_layout
-
-\begin_layout LyX-Code
- clone% run_tests tmp
-\end_layout
-
-\begin_layout LyX-Code
- clone% diff tmp test_output
-\end_layout
-
-\begin_layout LyX-Code
- You may get a few strange lines of the sort
-\end_layout
-
-\begin_layout LyX-Code
- clone% run_tests tmp
-\end_layout
-
-\begin_layout LyX-Code
- rm: tmp: No such file or directory
-\end_layout
-
-\begin_layout LyX-Code
- clone% diff tmp test_output
-\end_layout
-
-\begin_layout LyX-Code
- These should cause no concern.
- However, if the "diff" shows that
-\end_layout
-
-\begin_layout LyX-Code
- tmp and test_output are different, contact me (you have a
-\end_layout
-
-\begin_layout LyX-Code
- problem).
-
-\end_layout
-
-\begin_layout LyX-Code
- You should now be able to use scan_for_matches by following the
-\end_layout
-
-\begin_layout LyX-Code
- instructions given below (which is all the normal user should have
-\end_layout
-
-\begin_layout LyX-Code
- to understand, once things are installed properly).
-\end_layout
-
-\begin_layout LyX-Code
- ==============================================================
-\end_layout
-
-\begin_layout LyX-Code
-How to run scan_for_matches:
-\end_layout
-
-\begin_layout LyX-Code
- To run the program, you type need to create two files
-\end_layout
-
-\begin_layout LyX-Code
- 1.
- the first file contains the pattern you wish to scan for; I'll
-\end_layout
-
-\begin_layout LyX-Code
- call this file pat_file in what follows (but any name is ok)
-\end_layout
-
-\begin_layout LyX-Code
- 2.
- the second file contains a set of sequences to scan.
- These
-\end_layout
-
-\begin_layout LyX-Code
- should be in "fasta format".
- Just look at the contents of
-\end_layout
-
-\begin_layout LyX-Code
- test_dna_input to see examples of this format.
- Basically,
-\end_layout
-
-\begin_layout LyX-Code
- each sequence begins with a line of the form
-\end_layout
-
-\begin_layout LyX-Code
- >sequence_id
-\end_layout
-
-\begin_layout LyX-Code
- and is followed by one or more lines containing the sequence.
-\end_layout
-
-\begin_layout LyX-Code
- Once these files have been created, you just use
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches pat_file < input_file
-\end_layout
-
-\begin_layout LyX-Code
- to scan all of the input sequences for the given pattern.
- As an
-\end_layout
-
-\begin_layout LyX-Code
- example, suppose that pat_file contains a single line of the form
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...7 3...8 ~p1
-\end_layout
-
-\begin_layout LyX-Code
- Then,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- should produce two "hits".
- When I run this on my machine, I get
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[6,27]
-\end_layout
-
-\begin_layout LyX-Code
- cguaacc ggttaacc gguuacg
-\end_layout
-
-\begin_layout LyX-Code
- >tst2:[6,27]
-\end_layout
-
-\begin_layout LyX-Code
- CGUAACC GGTTAACC GGUUACG
-\end_layout
-
-\begin_layout LyX-Code
- clone%
-\end_layout
-
-\begin_layout LyX-Code
-Simple Patterns Built by Matching Ranges and Reverse Complements
-\end_layout
-
-\begin_layout LyX-Code
- Let me first explain this simple pattern:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...7 3...8 ~p1
-\end_layout
-
-\begin_layout LyX-Code
- The pattern consists of three "pattern units" separated by spaces.
-\end_layout
-
-\begin_layout LyX-Code
- The first pattern unit is
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...7
-\end_layout
-
-\begin_layout LyX-Code
- which means "match 4 to 7 characters and call them p1".
- The
-\end_layout
-
-\begin_layout LyX-Code
- second pattern unit is
-\end_layout
-
-\begin_layout LyX-Code
- 3...8
-\end_layout
-
-\begin_layout LyX-Code
- which means "then match 3 to 8 characters".
- The last pattern unit
-\end_layout
-
-\begin_layout LyX-Code
- is
-\end_layout
-
-\begin_layout LyX-Code
- ~p1
-\end_layout
-
-\begin_layout LyX-Code
- which means "match the reverse complement of p1".
- The first
-\end_layout
-
-\begin_layout LyX-Code
- reported hit is shown as
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[6,27]
-\end_layout
-
-\begin_layout LyX-Code
- cguaacc ggttaacc gguuacg
-\end_layout
-
-\begin_layout LyX-Code
- which states that characters 6 through 27 of sequence tst1 were
-\end_layout
-
-\begin_layout LyX-Code
- matched.
- "cguaac" matched the first pattern unit, "ggttaacc" the
-\end_layout
-
-\begin_layout LyX-Code
- second, and "gguuacg" the third.
- This is an example of a common
-\end_layout
-
-\begin_layout LyX-Code
- type of pattern used to search for sections of DNA or RNA that
-\end_layout
-
-\begin_layout LyX-Code
- would fold into a hairpin loop.
-\end_layout
-
-\begin_layout LyX-Code
-Searching Both Strands
-\end_layout
-
-\begin_layout LyX-Code
- Now for a short aside: scan_for_matches only searched the
-\end_layout
-
-\begin_layout LyX-Code
- sequences in the input file; it did not search the opposite
-\end_layout
-
-\begin_layout LyX-Code
- strand.
- With a pattern of the sort we just used, there is not
-\end_layout
-
-\begin_layout LyX-Code
- need o search the opposite strand.
- However, it is normally the
-\end_layout
-
-\begin_layout LyX-Code
- case that you will wish to search both the sequence and the
-\end_layout
-
-\begin_layout LyX-Code
- opposite strand (i.e., the reverse complement of the sequence).
-\end_layout
-
-\begin_layout LyX-Code
- To do that, you would just use the "-c" command line.
- For example,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches -c pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- Hits on the opposite strand will show a beginning location greater
-\end_layout
-
-\begin_layout LyX-Code
- than te end location of the match.
-\end_layout
-
-\begin_layout LyX-Code
-Defining Pairing Rules and Allowing Mismatches, Insertions, and Deletions
-\end_layout
-
-\begin_layout LyX-Code
- Let us stop now and ask "What additional features would one need to
-\end_layout
-
-\begin_layout LyX-Code
- really find the kinds of loop structures that characterize tRNAs,
-\end_layout
-
-\begin_layout LyX-Code
- rRNAs, and so forth?" I can immediately think of two:
-\end_layout
-
-\begin_layout LyX-Code
- a) you will need to be able to allow non-standard pairings
-\end_layout
-
-\begin_layout LyX-Code
- (those other than G-C and A-U), and
-\end_layout
-
-\begin_layout LyX-Code
- b) you will need to be able to tolerate some number of
-\end_layout
-
-\begin_layout LyX-Code
- mismatches and bulges.
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- Let me first show you how to handle non-standard "rules for
-\end_layout
-
-\begin_layout LyX-Code
- pairing in reverse complements".
- Consider the following pattern,
-\end_layout
-
-\begin_layout LyX-Code
- which I show as two line (you may use as many lines as you like in
-\end_layout
-
-\begin_layout LyX-Code
- forming a pattern, although you can only break a pattern at points
-\end_layout
-
-\begin_layout LyX-Code
- where space would be legal):
-\end_layout
-
-\begin_layout LyX-Code
- r1={au,ua,gc,cg,gu,ug,ga,ag}
-\end_layout
-
-\begin_layout LyX-Code
- p1=2...3 0...4 p2=2...5 1...5 r1~p2 0...4 ~p1
-\end_layout
-
-\begin_layout LyX-Code
- The first "pattern unit" does not actually match anything; rather,
-\end_layout
-
-\begin_layout LyX-Code
- it defines a "pairing rule" in which standard pairings are
-\end_layout
-
-\begin_layout LyX-Code
- allowed, as well as G-A and A-G (in case you wondered, Us and Ts
-\end_layout
-
-\begin_layout LyX-Code
- and upper and lower case can be used interchangably; for example
-\end_layout
-
-\begin_layout LyX-Code
- r1={AT,UA,gc,cg} could be used to define the "standard rule" for
-\end_layout
-
-\begin_layout LyX-Code
- pairings).
- The second line consists of six pattern units which
-\end_layout
-
-\begin_layout LyX-Code
- may be interpreted as follows:
-\end_layout
-
-\begin_layout LyX-Code
- p1=2...3 match 2 or 3 characters (call it p1)
-\end_layout
-
-\begin_layout LyX-Code
- 0...4 match 0 to 4 characters
-\end_layout
-
-\begin_layout LyX-Code
- p2=2...5 match 2 to 5 characters (call it p2)
-\end_layout
-
-\begin_layout LyX-Code
- 1...5 match 1 to 5 characters
-\end_layout
-
-\begin_layout LyX-Code
- r1~p2 match the reverse complement of p2,
-\end_layout
-
-\begin_layout LyX-Code
- allowing G-A and A-G pairs
-\end_layout
-
-\begin_layout LyX-Code
- 0...4 match 0 to 4 characters
-\end_layout
-
-\begin_layout LyX-Code
- ~p1 match the reverse complement of p1
-\end_layout
-
-\begin_layout LyX-Code
- allowing only G-C, C-G, A-T, and T-A pairs
-\end_layout
-
-\begin_layout LyX-Code
- Thus, r1~p2 means "match the reverse complement of p2 using rule r1".
-\end_layout
-
-\begin_layout LyX-Code
- Now let us consider the issue of tolerating mismatches and bulges.
-\end_layout
-
-\begin_layout LyX-Code
- You may add a "qualifier" to the pattern unit that gives the
-\end_layout
-
-\begin_layout LyX-Code
- tolerable number of "mismatches, deletions, and insertions".
-\end_layout
-
-\begin_layout LyX-Code
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- p1=10...10 3...8 ~p1[1,2,1]
-\end_layout
-
-\begin_layout LyX-Code
- means that the third pattern unit must match 10 characters,
-\end_layout
-
-\begin_layout LyX-Code
- allowing one "mismatch" (a pairing other than G-C, C-G, A-T, or
-\end_layout
-
-\begin_layout LyX-Code
- T-A), two deletions (a deletion is a character that occurs in p1,
-\end_layout
-
-\begin_layout LyX-Code
- but has been "deleted" from the string matched by ~p1), and one
-\end_layout
-
-\begin_layout LyX-Code
- insertion (an "insertion" is a character that occurs in the string
-\end_layout
-
-\begin_layout LyX-Code
- matched by ~p1, but not for which no corresponding character
-\end_layout
-
-\begin_layout LyX-Code
- occurs in p1).
- In this case, the pattern would match
-\end_layout
-
-\begin_layout LyX-Code
- ACGTACGTAC GGGGGGGG GCGTTACCT
-\end_layout
-
-\begin_layout LyX-Code
- which is, you must admit, a fairly weak loop.
- It is common to
-\end_layout
-
-\begin_layout LyX-Code
- allow mismatches, but you will find yourself using insertions and
-\end_layout
-
-\begin_layout LyX-Code
- deletions much more rarely.
- In any event, you should note that
-\end_layout
-
-\begin_layout LyX-Code
- allowing mismatches, insertions, and deletions does force the
-\end_layout
-
-\begin_layout LyX-Code
- program to try many additional possible pairings, so it does slow
-\end_layout
-
-\begin_layout LyX-Code
- things down a bit.
-\end_layout
-
-\begin_layout LyX-Code
-How Patterns Are Matched
-\end_layout
-
-\begin_layout LyX-Code
- Now is as good a time as any to discuss the basic flow of control
-\end_layout
-
-\begin_layout LyX-Code
- when matching patterns.
- Recall that a "pattern" is a sequence of
-\end_layout
-
-\begin_layout LyX-Code
- "pattern units".
- Suppose that the pattern units were
-\end_layout
-
-\begin_layout LyX-Code
- u1 u2 u3 u4 ...
- un
-\end_layout
-
-\begin_layout LyX-Code
- The scan of a sequence S begins by setting the current position
-\end_layout
-
-\begin_layout LyX-Code
- to 1.
- Then, an attempt is made to match u1 starting at the
-\end_layout
-
-\begin_layout LyX-Code
- current position.
- Each attempt to match a pattern unit can
-\end_layout
-
-\begin_layout LyX-Code
- succeed or fail.
- If it succeeds, then an attempt is made to match
-\end_layout
-
-\begin_layout LyX-Code
- the next unit.
- If it fails, then an attempt is made to find an
-\end_layout
-
-\begin_layout LyX-Code
- alternative match for the immediately preceding pattern unit.
- If
-\end_layout
-
-\begin_layout LyX-Code
- this succeeds, then we proceed forward again to the next unit.
- If
-\end_layout
-
-\begin_layout LyX-Code
- it fails we go back to the preceding unit.
- This process is called
-\end_layout
-
-\begin_layout LyX-Code
- "backtracking".
- If there are no previous units, then the current
-\end_layout
-
-\begin_layout LyX-Code
- position is incremented by one, and everything starts again.
- This
-\end_layout
-
-\begin_layout LyX-Code
- proceeds until either the current position goes past the end of
-\end_layout
-
-\begin_layout LyX-Code
- the sequence or all of the pattern units succeed.
- On success,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches reports the "hit", the current position is set
-\end_layout
-
-\begin_layout LyX-Code
- just past the hit, and an attempt is made to find another hit.
-\end_layout
-
-\begin_layout LyX-Code
- If you wish to limit the scan to simply finding a maximum of, say,
-\end_layout
-
-\begin_layout LyX-Code
- 10 hits, you can use the -n option (-n 10 would set the limit to
-\end_layout
-
-\begin_layout LyX-Code
- 10 reported hits).
- For example,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches -c -n 1 pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- would search for just the first hit (and would stop searching the
-\end_layout
-
-\begin_layout LyX-Code
- current sequences or any that follow in the input file).
-\end_layout
-
-\begin_layout LyX-Code
-Searching for repeats:
-\end_layout
-
-\begin_layout LyX-Code
- In the last section, I discussed almost all of the details
-\end_layout
-
-\begin_layout LyX-Code
- required to allow you to look for repeats.
- Consider the following
-\end_layout
-
-\begin_layout LyX-Code
- set of patterns:
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...6 3...8 p1 (find exact 6 character repeat separated
-\end_layout
-
-\begin_layout LyX-Code
- by to 8 characters)
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...6 3..8 p1[1,0,0] (allow one mismatch)
-\end_layout
-
-\begin_layout LyX-Code
- p1=3...3 p1[1,0,0] p1[1,0,0] p1[1,0,0]
-\end_layout
-
-\begin_layout LyX-Code
- (match 12 characters that are the remains
-\end_layout
-
-\begin_layout LyX-Code
- of a 3-character sequence occurring 4 times)
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...8 0...3 p2=6...8 p1 0...3 p2
-\end_layout
-
-\begin_layout LyX-Code
- (This would match things like
-\end_layout
-
-\begin_layout LyX-Code
- ATCT G TCTTT ATCT TG TCTTT
-\end_layout
-
-\begin_layout LyX-Code
- )
-\end_layout
-
-\begin_layout LyX-Code
-Searching for particular sequences:
-\end_layout
-
-\begin_layout LyX-Code
- Occasionally, one wishes to match a specific, known sequence.
-\end_layout
-
-\begin_layout LyX-Code
- In such a case, you can just give the sequence (along with an
-\end_layout
-
-\begin_layout LyX-Code
- optional statement of the allowable mismatches, insertions, and
-\end_layout
-
-\begin_layout LyX-Code
- deletions).
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...8 GAGA ~p1 (match a hairpin with GAGA as the loop)
-\end_layout
-
-\begin_layout LyX-Code
- RRRRYYYY (match 4 purines followed by 4 pyrimidines)
-\end_layout
-
-\begin_layout LyX-Code
- TATAA[1,0,0] (match TATAA, allowing 1 mismatch)
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-Matches against a "weight matrix":
-\end_layout
-
-\begin_layout LyX-Code
- I will conclude my examples of the types of pattern units
-\end_layout
-
-\begin_layout LyX-Code
- available for matching against nucleotide sequences by discussing a
-\end_layout
-
-\begin_layout LyX-Code
- crude implemetation of matching using a "weight matrix".
- While I
-\end_layout
-
-\begin_layout LyX-Code
- am less than overwhelmed with the syntax that I chose, I think that
-\end_layout
-
-\begin_layout LyX-Code
- the reader should be aware that I was thinking of generating
-\end_layout
-
-\begin_layout LyX-Code
- patterns containing such pattern units automatically from
-\end_layout
-
-\begin_layout LyX-Code
- alignments (and did not really plan on typing such things in by
-\end_layout
-
-\begin_layout LyX-Code
- hand very often).
- Anyway, suppose that you wanted to match a
-\end_layout
-
-\begin_layout LyX-Code
- sequence of eight characters.
- The "consensus" of these eight
-\end_layout
-
-\begin_layout LyX-Code
- characters is GRCACCGS, but the actual "frequencies of occurrence"
-\end_layout
-
-\begin_layout LyX-Code
- are given in the matrix below.
- Thus, the first character is an A
-\end_layout
-
-\begin_layout LyX-Code
- 16% the time and a G 84% of the time.
- The second is an A 57% of
-\end_layout
-
-\begin_layout LyX-Code
- the time, a C 10% of the time, a G 29% of the time, and a T 4% of
-\end_layout
-
-\begin_layout LyX-Code
- the time.
-
-\end_layout
-
-\begin_layout LyX-Code
- C1 C2 C3 C4 C5 C6 C7 C8
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- A 16 57 0 95 0 18 0 0
-\end_layout
-
-\begin_layout LyX-Code
- C 0 10 80 0 100 60 0 50
-\end_layout
-
-\begin_layout LyX-Code
- G 84 29 0 0 0 20 100 50
-\end_layout
-
-\begin_layout LyX-Code
- T 0 4 20 5 0 2 0 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- One could use the following pattern unit to search for inexact
-\end_layout
-
-\begin_layout LyX-Code
- matches related to such a "weight matrix":
-\end_layout
-
-\begin_layout LyX-Code
- {(16,0,84,0),(57,10,29,4),(0,80,0,20),(95,0,0,5),
-\end_layout
-
-\begin_layout LyX-Code
- (0,100,0,0),(18,60,20,2),(0,0,100,0),(0,50,50,0)} > 450
-\end_layout
-
-\begin_layout LyX-Code
- This pattern unit will attempt to match exactly eight characters.
-\end_layout
-
-\begin_layout LyX-Code
- For each character in the sequence, the entry in the corresponding
-\end_layout
-
-\begin_layout LyX-Code
- tuple is added to an accumulated sum.
- If the sum is greater than
-\end_layout
-
-\begin_layout LyX-Code
- 450, the match succeeds; else it fails.
-\end_layout
-
-\begin_layout LyX-Code
- Recently, this feature was upgraded to allow ranges.
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- 600 > {(16,0,84,0),(57,10,29,4),(0,80,0,20),(95,0,0,5),
-\end_layout
-
-\begin_layout LyX-Code
- (0,100,0,0),(18,60,20,2),(0,0,100,0),(0,50,50,0)} > 450
-\end_layout
-
-\begin_layout LyX-Code
- will work, as well.
-\end_layout
-
-\begin_layout LyX-Code
-Allowing Alternatives:
-\end_layout
-
-\begin_layout LyX-Code
- Very occasionally, you may wish to allow alternative pattern units
-\end_layout
-
-\begin_layout LyX-Code
- (i.e., "match either A or B").
- You can do this using something
-\end_layout
-
-\begin_layout LyX-Code
- like
-\end_layout
-
-\begin_layout LyX-Code
- ( GAGA | GCGCA)
-\end_layout
-
-\begin_layout LyX-Code
- which says "match either GAGA or GCGCA".
- You may take
-\end_layout
-
-\begin_layout LyX-Code
- alternatives of a list of pattern units, for example
-\end_layout
-
-\begin_layout LyX-Code
- (p1=3...3 3...8 ~p1 | p1=5...5 4...4 ~p1 GGG)
-\end_layout
-
-\begin_layout LyX-Code
- would match one of two sequences of pattern units.
- There is one
-\end_layout
-
-\begin_layout LyX-Code
- clumsy aspect of the syntax: to match a list of alternatives, you
-\end_layout
-
-\begin_layout LyX-Code
- need to fully the request.
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- (GAGA | (GCGCA | TTCGA))
-\end_layout
-
-\begin_layout LyX-Code
- would be needed to try the three alternatives.
-\end_layout
-
-\begin_layout LyX-Code
-One Minor Extension
-\end_layout
-
-\begin_layout LyX-Code
- Sometimes a pattern will contain a sequence of distinct ranges,
-\end_layout
-
-\begin_layout LyX-Code
- and you might wish to limit the sum of the lengths of the matched
-\end_layout
-
-\begin_layout LyX-Code
- subsequences.
- For example, suppose that you basically wanted to
-\end_layout
-
-\begin_layout LyX-Code
- match something like
-\end_layout
-
-\begin_layout LyX-Code
- ARRYYTT p1=0...5 GCA[1,0,0] p2=1...6 ~p1 4...8 ~p2 p3=4...10 CCT
-\end_layout
-
-\begin_layout LyX-Code
- but that the sum of the lengths of p1, p2, and p3 must not exceed
-\end_layout
-
-\begin_layout LyX-Code
- eight characters.
- To do this, you could add
-\end_layout
-
-\begin_layout LyX-Code
- length(p1+p2+p3) < 9
-\end_layout
-
-\begin_layout LyX-Code
- as the last pattern unit.
- It will just succeed or fail (but does
-\end_layout
-
-\begin_layout LyX-Code
- not actually match any characters in the sequence).
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-Matching Protein Sequences
-\end_layout
-
-\begin_layout LyX-Code
- Suppose that the input file contains protein sequences.
- In this
-\end_layout
-
-\begin_layout LyX-Code
- case, you must invoke scan_for_matches with the "-p" option.
- You
-\end_layout
-
-\begin_layout LyX-Code
- cannot use aspects of the language that relate directly to
-\end_layout
-
-\begin_layout LyX-Code
- nucleotide sequences (e.g., the -c command line option or pattern
-\end_layout
-
-\begin_layout LyX-Code
- constructs referring to the reverse complement of a previously
-\end_layout
-
-\begin_layout LyX-Code
- matched unit).
-
-\end_layout
-
-\begin_layout LyX-Code
- You also have two additional constructs that allow you to match
-\end_layout
-
-\begin_layout LyX-Code
- either "one of a set of amino acids" or "any amino acid other than
-\end_layout
-
-\begin_layout LyX-Code
- those a given set".
- For example,
-\end_layout
-
-\begin_layout LyX-Code
- p1=0...4 any(HQD) 1...3 notany(HK) p1
-\end_layout
-
-\begin_layout LyX-Code
- would successfully match a string like
-\end_layout
-
-\begin_layout LyX-Code
- YWV D AA C YWV
-\end_layout
-
-\begin_layout LyX-Code
-Using the show_hits Utility
-\end_layout
-
-\begin_layout LyX-Code
- When viewing a large set of complex matches, you might find it
-\end_layout
-
-\begin_layout LyX-Code
- convenient to post-process the scan_for_matches output to get a
-\end_layout
-
-\begin_layout LyX-Code
- more readable version.
- We provide a simple post-processor called
-\end_layout
-
-\begin_layout LyX-Code
- "show_hits".
- To see its effect, just pipe the output of a
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches into show_hits:
-\end_layout
-
-\begin_layout LyX-Code
- Normal Output:
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches -c pat_file < tmp
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[1,28]
-\end_layout
-
-\begin_layout LyX-Code
- gtacguaacc ggttaac cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[28,1]
-\end_layout
-
-\begin_layout LyX-Code
- gtacgtaacc ggttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- >tst2:[2,31]
-\end_layout
-
-\begin_layout LyX-Code
- CGTACGUAAC C GGTTAACC GGUUACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- >tst2:[31,2]
-\end_layout
-
-\begin_layout LyX-Code
- CGTACGTAAC C GGTTAACC GGTTACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- >tst3:[3,32]
-\end_layout
-
-\begin_layout LyX-Code
- gtacguaacc g gttaactt cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- >tst3:[32,3]
-\end_layout
-
-\begin_layout LyX-Code
- gtacgtaacc g aagttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- Piped Through show_hits:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches -c pat_file < tmp | show_hits
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[1,28]: gtacguaacc ggttaac cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[28,1]: gtacgtaacc ggttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[2,31]: CGTACGUAAC C GGTTAACC GGUUACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[31,2]: CGTACGTAAC C GGTTAACC GGTTACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[3,32]: gtacguaacc g gttaactt cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[32,3]: gtacgtaacc g aagttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- clone%
-\end_layout
-
-\begin_layout LyX-Code
- Optionally, you can specify which of the "fields" in the matches
-\end_layout
-
-\begin_layout LyX-Code
- you wish to sort on, and show_hits will sort them.
- The field
-\end_layout
-
-\begin_layout LyX-Code
- numbers start with 0.
- So, you might get something like
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches -c pat_file < tmp | show_hits 2 1
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[2,31]: CGTACGUAAC C GGTTAACC GGUUACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[31,2]: CGTACGTAAC C GGTTAACC GGTTACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[32,3]: gtacgtaacc g aagttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[1,28]: gtacguaacc ggttaac cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[28,1]: gtacgtaacc ggttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[3,32]: gtacguaacc g gttaactt cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- clone%
-\end_layout
-
-\begin_layout LyX-Code
- In this case, the hits have been sorted on fields 2 and 1 (that is,
-\end_layout
-
-\begin_layout LyX-Code
- the third and second matched subfields).
-\end_layout
-
-\begin_layout LyX-Code
- show_hits is just one possible little post-processor, and you
-\end_layout
-
-\begin_layout LyX-Code
- might well wish to write a customized one for yourself.
-\end_layout
-
-\begin_layout LyX-Code
-Reducing the Cost of a Search
-\end_layout
-
-\begin_layout LyX-Code
- The scan_for_matches utility uses a fairly simple search, and may
-\end_layout
-
-\begin_layout LyX-Code
- consume large amounts of CPU time for complex patterns.
- Someday,
-\end_layout
-
-\begin_layout LyX-Code
- I may decide to optimize the code.
- However, until then, let me
-\end_layout
-
-\begin_layout LyX-Code
- mention one useful technique.
-
-\end_layout
-
-\begin_layout LyX-Code
- When you have a complex pattern that includes a number of varying
-\end_layout
-
-\begin_layout LyX-Code
- ranges, imprecise matches, and so forth, it is useful to
-\end_layout
-
-\begin_layout LyX-Code
- "pipeline" matches.
- That is, form a simpler pattern that can be
-\end_layout
-
-\begin_layout LyX-Code
- used to scan through a large database extracting sections that
-\end_layout
-
-\begin_layout LyX-Code
- might be matched by the more complex pattern.
- Let me illustrate
-\end_layout
-
-\begin_layout LyX-Code
- with a short example.
- Suppose that you really wished to match the
-\end_layout
-
-\begin_layout LyX-Code
- pattern
-\end_layout
-
-\begin_layout LyX-Code
- p1=3...5 0...8 ~p1[1,1,0] p2=6...7 3...6 AGC 3...5 RYGC ~p2[1,0,0]
-\end_layout
-
-\begin_layout LyX-Code
- In this case, the pattern units AGC 3...5 RYGC can be used to rapidly
-\end_layout
-
-\begin_layout LyX-Code
- constrain the overall search.
- You can preprocess the overall
-\end_layout
-
-\begin_layout LyX-Code
- database using the pattern:
-\end_layout
-
-\begin_layout LyX-Code
- 31...31 AGC 3...5 RYGC 7...7
-\end_layout
-
-\begin_layout LyX-Code
- Put the complex pattern in pat_file1 and the simpler pattern in
-\end_layout
-
-\begin_layout LyX-Code
- pat_file2.
- Then use,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches -c pat_file2 < nucleotide_database |
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches pat_file1
-\end_layout
-
-\begin_layout LyX-Code
- The output will show things like
-\end_layout
-
-\begin_layout LyX-Code
- >seqid:[232,280][2,47]
-\end_layout
-
-\begin_layout LyX-Code
- matches pieces
-\end_layout
-
-\begin_layout LyX-Code
- Then, the actual section of the sequence that was matched can be
-\end_layout
-
-\begin_layout LyX-Code
- easily computed as [233,278] (remember, the positions start from
-\end_layout
-
-\begin_layout LyX-Code
- 1, not 0).
-\end_layout
-
-\begin_layout LyX-Code
- Let me finally add, you should do a few short experiments to see
-\end_layout
-
-\begin_layout LyX-Code
- whether or not such pipelining actually improves performance -- it
-\end_layout
-
-\begin_layout LyX-Code
- is not always obvious where the time is going, and I have
-\end_layout
-
-\begin_layout LyX-Code
- sometimes found that the added complexity of pipelining actually
-\end_layout
-
-\begin_layout LyX-Code
- slowed things up.
- It gets its best improvements when there are
-\end_layout
-
-\begin_layout LyX-Code
- exact matches of more than just a few characters that can be
-\end_layout
-
-\begin_layout LyX-Code
- rapidly used to eliminate large sections of the database.
-\end_layout
-
-\begin_layout LyX-Code
-=============
-\end_layout
-
-\begin_layout LyX-Code
-Additions:
-\end_layout
-
-\begin_layout LyX-Code
-Feb 9, 1995: the pattern units ^ and $ now work as in normal regular
-\end_layout
-
-\begin_layout LyX-Code
- expressions.
- That is
-\end_layout
-
-\begin_layout LyX-Code
- TTF $
-\end_layout
-
-\begin_layout LyX-Code
- matches only TTF at the end of the string and
-\end_layout
-
-\begin_layout LyX-Code
- ^ TTF
-\end_layout
-
-\begin_layout LyX-Code
- matches only an initial TTF
-\end_layout
-
-\begin_layout LyX-Code
- The pattern unit
-\end_layout
-
-\begin_layout LyX-Code
- <p1
-\end_layout
-
-\begin_layout LyX-Code
- matches the reverse of the string named p1.
- That is,
-\end_layout
-
-\begin_layout LyX-Code
- if p1 matched GCAT, then <p1 would match TACG.
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...6 <p1
-\end_layout
-
-\begin_layout LyX-Code
- matches a real palindrome (not the biologically common
-\end_layout
-
-\begin_layout LyX-Code
- meaning of "reverse complement")
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\end_body
-\end_document
+++ /dev/null
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
-\begin_document
-\begin_header
-\textclass scrartcl
-\begin_preamble
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-\author ""
-\author ""
-\end_header
-
-\begin_body
-
-\begin_layout Title
-Biotools Cookbook
-\end_layout
-
-\begin_layout Author
-Martin Asser Hansen
-\end_layout
-
-\begin_layout Publishers
-John Mattick Group
-\newline
-Institute for Molecular Bioscience
-\newline
-University of Queensland
-\newline
-Aust
-ralia
-\newline
-E-mail: mail@maasha.dk
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
-
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-thispagestyle{empty}
-\end_layout
-
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-
-
-\end_layout
-
-\begin_layout Standard
-
-\newpage
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset LatexCommand tableofcontents
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset FloatList figure
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-
-\newpage
-
-\end_layout
-
-\begin_layout Section
-Introduction
-\end_layout
-
-\begin_layout Standard
-Biotools is a selection of simple tools that can be linked together (piped
- as we shall call it) in a very flexible manner to perform both simple and
- complex tasks.
- The fundamental idea is that biotools work on a data stream that will only
- terminate at the end of an analysis and that this data stream can be passed
- through several different biotools, each performing one specific task.
- The advantage of this approach is that a user can perform simple and complex
- tasks without having to write advanced code.
- Moreover, since the data format used to pass data between biotools is text
- based, biotools can be written by different developers in their favorite
- programming language --- and still the biotools will be able to work together.
-\end_layout
-
-\begin_layout Standard
-In the most simple form bioools can be piped together on the command line
- like this (using the pipe character '|'):
-\end_layout
-
-\begin_layout LyX-Code
-read_data | calculate_something | write_result
-\end_layout
-
-\begin_layout Standard
-However, a more comprehensive analysis could be composed:
-\end_layout
-
-\begin_layout LyX-Code
-read_data | select_entries | convert_entries | search_database
-\end_layout
-
-\begin_layout LyX-Code
-evaluate_results | plot_diagram | plot_another_diagram |
-\end_layout
-
-\begin_layout LyX-Code
-load_to_database
-\end_layout
-
-\begin_layout Standard
-The data stream that is piped through the biotools consists of records of
- key/value pairs in the same way a hash does in order to keep as simple
- a structure as possible.
- An example record can be seen below:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-REC_TYPE: PATSCAN
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-MATCH: AGATCAAGTG
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-S_BEG: 7
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-S_END: 16
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-ALIGN_LEN: 9
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-S_ID: piR-t6
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-STRAND: +
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-PATTERN: AGATCAAGTG
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
----
-\end_layout
-
-\begin_layout Standard
-The '
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-' denotes the delimiter of the records, and each key is a word followed
- by a ':' and a white-space and then the value.
- By convention the biotools only uses upper case keys (a list of used keys
- can be seen in Appendix\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sec:Keys"
-
-\end_inset
-
-).
- Since the records basically are hash structures this mean that the order
- of the keys in the stream is unordered, and in the above example it is
- pure coincidence that HIT_BEG is displayed before HIT_END, however, when
- the order of the keys is importent, the biotools will automagically see
- to that.
-\end_layout
-
-\begin_layout Standard
-All of the biotools are able to read and write a data stream to and from
- file as long as the records are in the biotools format.
- This means that if you are undertaking a lengthy analysis where one of
- the steps is time consuming, you may save the stream after this step, and
- subsequently start one or more analysis from that last step
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-It is a goal that the biotools at some point will be able to dump the data
- stream to file in case one of the tools fail critically.
-\end_layout
-
-\end_inset
-
-.
- If you are running a lengthy analysis it is highly recommended that you
- create a small test sample of the data and run that through the pipeline
- --- and once you are satisfied with the result proceed with the full data
- set (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-select-a-few-records"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Standard
-All of the biotools can be supplied with long arguments prefixed with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
- switches or single character arguments prefixed with - switches that can
- be grouped together (e.g.
- -xok).
- In this cookbook only the long switches are used to emphasize what these
- switches do.
-\end_layout
-
-\begin_layout Section
-Setup
-\end_layout
-
-\begin_layout Standard
-In order to get the biotools to work, you need to add environment settings
- to include the code binaries, scripts, and modules that constitute the
- biotools package.
- Assuming that you are using bash, add the following to your '~/.bashrc'
- file using your favorite editor.
- After the changes has been saved you need to either run 'source ~/.bashrc'
- or relogin.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-if [ -f "/home/m.hansen/maasha/conf/bashrc" ]; then
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- source "/home/m.hansen/maasha/conf/bashrc"
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-fi
-\end_layout
-
-\begin_layout Section
-Getting Started
-\end_layout
-
-\begin_layout Standard
-The biotool
-\series bold
-list_biotools
-\series default
- lists all the biotools along with a description:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-list_biotools
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-align_seq Align sequences in stream using Muscle.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-analyze_seq Analysis the residue composition of each sequence
- in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-analyze_vals Determine type, count, min, max, sum and mean for
- values in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-blast_seq BLAST sequences in stream against a specified database.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-blat_seq BLAT sequences in stream against a specified genome.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-complement_seq Complement sequences in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_records Count the number of records in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_seq Count sequences in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_vals Count the number of times values of given keys exists
- in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-create_blast_db Create a BLAST database from sequences in stream for
- use with BLAST.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-...
-\end_layout
-
-\begin_layout Standard
-To list the biotools for writing different formats, you can use unix's grep
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-list_biotools | grep write
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_align Write aligned sequences in pretty alignment format.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_bed Write records from stream as BED lines.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_blast Write BLAST records from stream in BLAST tabular format
- (-m8 and 9).
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_fasta Write sequences in FASTA format.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_psl Write records from stream in PSL format.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_tab Write records from stream as tab separated table.
-\end_layout
-
-\begin_layout Standard
-In order to find out how a specific biotool works, you just type the program
- name without any arguments and press return and the usage of the biotool
- will be displayed.
- E.g.
-
-\series bold
-read_fasta
-\series default
- <return>:
-\end_layout
-
-\begin_layout Standard
-\begin_inset Box Frameless
-position "t"
-hor_pos "c"
-has_inner_box 1
-inner_pos "t"
-use_parbox 0
-width "100col%"
-special "none"
-height "1in"
-height_special "totalheight"
-status open
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Program name: read_fasta
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Contact: mail@maasha.dk
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Date: August 2007
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/
-gpl.html)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Description: Read FASTA entries.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Usage: read_fasta [options] -i <FASTA file(s)>
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Options:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-i <file(s)> | --data_in=<file(s)>] - Comma separated list of files
- to read.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-n <int> | --num=<int>] - Limit number of records to read.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-I <file> | --stream_in=<file>] - Read input stream from file
- - Default=STDIN
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-O <file> | --stream_out=<file>] - Write output stream to file
- - Default=STDOUT
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Examples:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i test.fna - Read FASTA entries from file.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i test1.fna,test2,fna - Read FASTA entries from files.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i '*.fna' - Read FASTA entries from files.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i test.fna -n 10 - Read first 10 FASTA entries from
- file.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Section
-The Data Stream
-\end_layout
-
-\begin_layout Subsection
-How to read the data stream from file?
-\begin_inset LatexCommand label
-name "sub:How-to-read-stream"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-You want to read a data stream that you previously have saved to file in
- biotools format.
- This can be done implicetly or explicitly.
- The implicit way uses the 'stdout' stream of the Unix terminal:
-\end_layout
-
-\begin_layout LyX-Code
-cat | <biotool>
-\end_layout
-
-\begin_layout Standard
-cat is the Unix command that reads a file and output the result to 'stdout'
- --- which in this case is piped to any biotool represented by the <biotool>.
- It is also possible to read the data stream using '<' to direct the 'stdout'
- stream into the biotool like this:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> < <file>
-\end_layout
-
-\begin_layout Standard
-However, that will not work if you pipe more biotools together.
- Then it is much safer to read the stream from a file explicitly like this:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --stream_in=<file>
-\end_layout
-
-\begin_layout Standard
-Here the filename <file> is explicetly given to the biotool <biotool> with
- the switch
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_in.
- This switch works with all biotools.
- It is also possible to read in data from multiple sources by repeating
- the explicit read step:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --stream_in=<file1> | <biotool> --stream_in=<file2>
-\end_layout
-
-\begin_layout Subsection
-How to write the data stream to file?
-\begin_inset LatexCommand label
-name "sub:How-to-write-stream"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-In order to save the output stream from a biotool to file, so you can read
- in the stream again at a later time, you can do one of two things:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> > <file>
-\end_layout
-
-\begin_layout Standard
-All, the biotools write the data stream to 'stdout' by default which can
- be written to a file by redirecting 'stdout' to file using '>' , however,
- if one of the biotools for writing other formats is used then the both
- the biotools records as well as the result output will go to 'stdout' in
- a mixture causing havock! To avoid this you must use the switch
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_out that explictly tells the biotool to write the output stream to
- file:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --stream_out=<file>
-\end_layout
-
-\begin_layout Standard
-The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_out switch works with all biotools.
-\end_layout
-
-\begin_layout Subsection
-How to terminate the data stream?
-\end_layout
-
-\begin_layout Standard
-The data stream is never stops unless the user want to save the stream or
- by supplying the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch that will terminate the stream:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --no_stream
-\end_layout
-
-\begin_layout Standard
-The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch only works with those biotools where it makes sense that
- the user might want to terminale the data stream,
-\emph on
-i.e
-\emph default
-.
- after an analysis step where the user wants to output the result, but not
- the data stream.
-\end_layout
-
-\begin_layout Subsection
-How to write my results to file?
-\begin_inset LatexCommand label
-name "sub:How-to-write-result"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Saving the result of an analysis to file can be done implicitly or explicitly.
- The implicit way:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --no_stream > <file>
-\end_layout
-
-\begin_layout Standard
-If you use '>' to redirect 'stdout' to file then it is important to use
- the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch to avoid writing a mix of biotools records and result to
- the same file causing havock.
- The safe way is to use the
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out switch which explicetly tells the biotool to write the result
- to a given file:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --result_out=<file>
-\end_layout
-
-\begin_layout Standard
-Using the above method will not terminate the stream, so it is possible
- to pipe that into another biotool generating different results:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool1> --result_out=<file1> | <biotool2> --result_out=<file2>
-\end_layout
-
-\begin_layout Standard
-And still the data stream will continue unless terminated with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --result_out=<file> --no_stream
-\end_layout
-
-\begin_layout Standard
-Or written to file using implicitly or explicity
-\begin_inset LatexCommand eqref
-reference "sub:How-to-write-result"
-
-\end_inset
-
-.
- The explicit way:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --result_out=<file1> --stream_out=<file2>
-\end_layout
-
-\begin_layout Subsection
-How to read data from multiple sources?
-\end_layout
-
-\begin_layout Standard
-To read multiple data sources, with the same type or different type of data
- do:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool1> --data_in=<file1> | <biotool2> --data_in=<file2>
-\end_layout
-
-\begin_layout Standard
-where type is the data type a specific biotool reads.
-\end_layout
-
-\begin_layout Section
-Reading input
-\end_layout
-
-\begin_layout Subsection
-How to read biotools input?
-\end_layout
-
-\begin_layout Standard
-See
-\begin_inset LatexCommand eqref
-reference "sub:How-to-read-stream"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Subsection
-How to read in data?
-\end_layout
-
-\begin_layout Standard
-Data in different formats can be read with the appropriate biotool for that
- format.
- The biotools are typicalled named 'read_<data type>' such as
-\series bold
-read_fasta
-\series default
-,
-\series bold
-read_bed
-\series default
-,
-\series bold
-read_tab
-\series default
-, etc., and all behave in a similar manner.
- Data can be read by supplying the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-data_in switch and a file name to the file containing the data:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --data_in=<file>
-\end_layout
-
-\begin_layout Standard
-It is also possible to read in a saved biotools stream (see
-\begin_inset LatexCommand ref
-reference "sub:How-to-read-stream"
-
-\end_inset
-
-) as well as reading data in one go:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --stream_in=<file1> --data_in=<file2>
-\end_layout
-
-\begin_layout Standard
-If you want to read data from several files you can do this:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --data_in=<file1> | <biotool> --data_in=<file2>
-\end_layout
-
-\begin_layout Standard
-If you have several data files you can read in all explicitly with a comma
- separated list:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --data_in=file1,file2,file3
-\end_layout
-
-\begin_layout Standard
-And it is also possible to use file globbing
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-using the short option will only work if you quote the argument -i '*.fna'
-\end_layout
-
-\end_inset
-
-:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --data_in=*.fna
-\end_layout
-
-\begin_layout Standard
-Or in a combination:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --data_in=file1,/dir/*.fna
-\end_layout
-
-\begin_layout Standard
-Finally, it is possible to read in data in different formats using the appropria
-te biotool for each format:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool1> --data_in=<file1> | <biotool2> --data_in=<file2> ...
-\end_layout
-
-\begin_layout Subsection
-How to read FASTA input?
-\end_layout
-
-\begin_layout Standard
-Sequences in FASTA format can be read explicitly using
-\series bold
-read_fasta
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file>
-\end_layout
-
-\begin_layout Subsection
-How to read alignment input?
-\end_layout
-
-\begin_layout Standard
-If your alignment if FASTA formatted then you can
-\series bold
-read_align
-\series default
-.
- It is also possible to use
-\series bold
-read_fasta
-\series default
- since the data is FASTA formatted, however, with
-\series bold
-read_fasta
-\series default
- the key ALIGN will be omitted.
- The ALIGN key is used to determine which sequences belong to what alignment
- which is required for
-\series bold
-write_align
-\series default
-.
-\end_layout
-
-\begin_layout LyX-Code
-read_align --data_in=<file>
-\end_layout
-
-\begin_layout Subsection
-How to read tabular input?
-\begin_inset LatexCommand label
-name "sub:How-to-read-table"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Tabular input can be read with
-\series bold
-read_tab
-\series default
- which will read in all rows and chosen columns (separated by a given delimter)
- from a table in text format.
-\end_layout
-
-\begin_layout Standard
-The table below:
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Tabular
-<lyxtabular version="3" rows="4" columns="3">
-<features>
-<column alignment="left" valignment="top" width="0">
-<column alignment="left" valignment="top" width="0">
-<column alignment="left" valignment="top" width="0">
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Human
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-ATACGTCAG
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-23524
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Dog
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-AGCATGAC
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-2442
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Mouse
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-GACTG
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-234
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Cat
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-AAATGCA
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-2342
-\end_layout
-
-\end_inset
-</cell>
-</row>
-</lyxtabular>
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Can be read using the command:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file>
-\end_layout
-
-\begin_layout Standard
-Which will result in four records, one for each row, where the keys V0,
- V1, V2 are the default keys for the organism, sequence, and count, respectively.
- It is possible to select a subset of colums to read by using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-cols switch which takes a comma separated list of columns numbers (first
- column is designated 0) as argument.
- So to read in only the sequence and the count so that the count comes before
- the sequence do:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file> --cols=2,1
-\end_layout
-
-\begin_layout Standard
-It is also possible to name the columns with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys switch:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file> --cols=2,1 --keys=COUNT,SEQ
-\end_layout
-
-\begin_layout Subsection
-How to read BED input?
-\end_layout
-
-\begin_layout Standard
-The BED (Browser Extensible Data
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://genome.ucsc.edu/FAQ/FAQformat"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-) format is a tabular format for data pertaining to one of the Eukaryotic
- genomes in the UCSC genome brower
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://genome.ucsc.edu/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-.
- The BED format consists of up to 12 columns, where the first three are
- mandatory CHR, CHR_BEG, and CHR_END.
- The mandatory columns and any of the optional columns can all be read in
- easily with the
-\series bold
-read_bed
-\series default
- biotool.
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<file>
-\end_layout
-
-\begin_layout Standard
-It is also possible to read the BED file with
-\series bold
-read_tab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-read-table"
-
-\end_inset
-
-), however, that will be more cumbersome because you need to specify the
- keys:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file> --keys=CHR,CHR_BEG,CHR_END ...
-\end_layout
-
-\begin_layout Subsection
-How to read PSL input?
-\end_layout
-
-\begin_layout Standard
-The PSL format is the output from BLAT and contains 21 mandatory fields
- that can be read with
-\series bold
-read_psl
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-read_psl --data_in=<file>
-\end_layout
-
-\begin_layout Section
-Writing output
-\end_layout
-
-\begin_layout Standard
-All result output can be written explicitly to file using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out switch which all result generating biotools have.
- It is also possible to write the result to file implicetly by directing
- 'stdout' to file using '>', however, that requires the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream swich to prevent a mixture of data stream and results in the file.
- The explicit (and safe) way:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | <biotool> --result_out=<file>
-\end_layout
-
-\begin_layout Standard
-The implicit way:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | <biotool> --no_stream > <file>
-\end_layout
-
-\begin_layout Subsection
-How to write biotools output?
-\end_layout
-
-\begin_layout Standard
-See
-\begin_inset LatexCommand eqref
-reference "sub:How-to-write-stream"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Subsection
-How to write FASTA output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-fasta"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-FASTA output can be written with
-\series bold
-write_fasta
-\series default
-.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_fasta --result_out=<file>
-\end_layout
-
-\begin_layout Standard
-It is also possible to wrap the sequences to a given width using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-wrap switch allthough wrapping of sequence is generally an evil thing:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_fasta --no_stream --wrap=80
-\end_layout
-
-\begin_layout Subsection
-How to write alignment output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-alignment"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Pretty alignments with ruler
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-'.' for every 10 residues, ':' for every 50, and '|' for every 100
-\end_layout
-
-\end_inset
-
- and consensus sequence
-\begin_inset Note Note
-status collapsed
-
-\begin_layout Standard
-which reminds me to make that an option.
-\end_layout
-
-\end_inset
-
- can be created with
-\series bold
-write_align
-\series default
-, what also have the optional
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-wrap switch to break the alignment into blocks of a given width:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_align --result_out=<file> --wrap=80
-\end_layout
-
-\begin_layout Standard
-If the number of sequnces in the alignment is 2 then a pairwise alignment
- will be output otherwise a multiple alignment.
- And if the sequence type, determined automagically, is protein, then residues
- and symbols (+,\InsetSpace ~
-:,\InsetSpace ~
-.) will be used to show consensus according to the Blosum62
- matrix.
-\end_layout
-
-\begin_layout Subsection
-How to write tabular output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-tab"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Outputting the data stream as a table can be done with
-\series bold
-write_tab
-\series default
-, which will write generate one row per record with the values as columns.
- If you supply the optional
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-comment switch, when the first row in the table will be a 'comment' line
- prefixed with a '#':
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --comment
-\end_layout
-
-\begin_layout Standard
-You can also change the delimiter from the default (tab) to
-\emph on
-e.g.
-
-\emph default
- ',':
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --delimit=','
-\end_layout
-
-\begin_layout Standard
-If you want the values output in a specific order you have to supply a comma
- separated list using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys switch that will print only those keys in that order:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --keys=SEQ_NAME,COUNT
-\end_layout
-
-\begin_layout Standard
-Alternatively, if you have some keys that you don't want in the tabular
- output, use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_keys switch.
- So to print all keys except SEQ and SEQ_TYPE do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --no_keys=SEQ,SEQ_TYPE
-\end_layout
-
-\begin_layout Standard
-Finally, if you have a stream containing a mix of different records types,
-
-\emph on
-e.g.
-
-\emph default
- records with sequences and records with matches, then you can use
-\series bold
-write_tab
-\series default
- to output all the records in tabluar format, however, the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-comment,
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys, and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_keys switches will only respond to records of the first type encountered.
- The reason is that outputting mixed records is probably not what you want
- anyway, and you should remove all the unwanted records from the stream
- before outputting the table:
-\series bold
-grab
-\series default
- is your friend (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-grab"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to write a BED output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-BED"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Data in BED format can be output if the records contain the mandatory keys
- CHR, CHR_BEG, and CHR_END using
-\series bold
-write_bed
-\series default
-.
- If the optional keys are also present, they will be output as well:
-\end_layout
-
-\begin_layout LyX-Code
-write_bed --result_out=<file>
-\end_layout
-
-\begin_layout Subsection
-How to write PSL output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-PSL"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Data in PSL format can be output using
-\series bold
-write_psl:
-\end_layout
-
-\begin_layout LyX-Code
-write_psl --result_out=<file>
-\end_layout
-
-\begin_layout Section
-Manipulating Records
-\end_layout
-
-\begin_layout Subsection
-How to select a few records?
-\begin_inset LatexCommand label
-name "sub:How-to-select-a-few-records"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-To quickly get an overview of your data you can limit the data stream to
- show a few records.
- This also very useful to test the pipeline with a few records if you are
- setting up a complex analysis using several biotools.
- That way you can inspect that all goes well before analyzing and waiting
- for the full data set.
- All of the read_<type> biotools have the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num switch which will take a number as argument and only that number of
- records will be read.
- So to read in the first 10 FASTA entries from a file:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna --num=10
-\end_layout
-
-\begin_layout Standard
-Another way of doing this is to use
-\series bold
-head_records
-\series default
- will limit the stream to show the first 10 records (default):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | head_records
-\end_layout
-
-\begin_layout Standard
-Using
-\series bold
-head_records
-\series default
- directly after one of the read_<type> biotools will be a lot slower than
- using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num switch with the read_<type> biotools, however,
-\series bold
-head_records
-\series default
- can also be used to limit the output from all the other biotools.
- It is also possible to give
-\series bold
-head_records
-\series default
- a number of records to show using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num switch.
- So to display the first 100 records do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | head_records --num=100
-\end_layout
-
-\begin_layout Subsection
-How to select random records?
-\begin_inset LatexCommand label
-name "sub:How-to-select-random-records"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-If you want to inspect a number of random records from the stream this can
- be done with the
-\series bold
-random_records
-\series default
- biotool.
- So if you have 1 mio records in the stream and you want to select 1000
- random records do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | random_records --num=1000
-\end_layout
-
-\begin_layout Subsection
-How to count all records in the data stream?
-\end_layout
-
-\begin_layout Standard
-To count all the records in the data stream use
-\series bold
-count_records
-\series default
-, which adds one record (which is not included in the count) to the data
- stream.
- So to count the number of sequences in a FASTA file you can do this:
-\end_layout
-
-\begin_layout LyX-Code
-cat test.fna | read_fasta | count_records --no_stream
-\end_layout
-
-\begin_layout Standard
-Which will write the last record containing the count to 'stdout':
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_records: 630
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
----
-\end_layout
-
-\begin_layout Standard
-It is also possible to write the count to file using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out switch.
-\end_layout
-
-\begin_layout Subsection
-How to get the length of record values?
-\begin_inset LatexCommand label
-name "sub:How-to-get-value_length"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Use the
-\series bold
-length_vals
-\series default
- biotool to get the length of each value for a comma separated list of keys:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | length_vals --keys=HIT,PATTERN
-\end_layout
-
-\begin_layout Subsection
-How to grab specific records?
-\begin_inset LatexCommand label
-name "sub:How-to-grab"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The biotool
-\series bold
-grab
-\series default
- is related to the Unix grep and locates records based on matching keys
- and/or values using either a pattern, a Perl regex, or a numerical evaluation.
- To easily
-\series bold
-grab
-\series default
- all records in the stream that has any mentioning of the pattern 'human'
- just pipe the data stream through
-\series bold
-grab
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human
-\end_layout
-
-\begin_layout Standard
-This will search for the pattern 'human' in all keys and all values.
- The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern switch takes a comma separated list of patterns, so in order to
- match multiple patterns do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human,mouse
-\end_layout
-
-\begin_layout Standard
-It is also possible to use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in switch instead of
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern.
-
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in is used to read a file with one pattern per line:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern_in=patterns.txt
-\end_layout
-
-\begin_layout Standard
-If you want the opposite result --- to find all records that does not match
- the patterns, add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-invert switch, which not only works with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern switch, but also with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-regex and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-eval:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human --invert
-\end_layout
-
-\begin_layout Standard
-If you want to search the record keys only,
-\emph on
-e.g.
-
-\emph default
- to find all records containing the key SEQ you can add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys_only switch.
- This will prevent matching of SEQ in any record value, and in fact SEQ
- is a not uncommon peptide sequence you could get an unwanted record.
- Also, this will give an increase in speed since only the keys are searched:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=SEQ --keys_only
-\end_layout
-
-\begin_layout Standard
-However, if you are interested in finding the peptide sequence SEQ and not
- the SEQ key, just add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-vals_only switch instead:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=SEQ --vals_only
-\end_layout
-
-\begin_layout Standard
-Also, if you want to grab for certain key/value pairs you can supply a comma
- separated list of keys whos values will then be searched using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys switch.
- This is handy if your records contain large genomic sequences and you dont
- want to search the entire sequence for
-\emph on
-e.g.
-
-\emph default
- the organism name --- it is much faster to tell
-\series bold
-grab
-\series default
- which keys to search the value for:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human --keys=SEQ_NAME
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout Standard
-It is also possible to invoke flexible matching using regex (regular expressions
-) instead of simple pattern matching.
- In
-\series bold
-grab
-\series default
- the regex engine is Perl based and allows use of different type of wild
- cards, alternatives,
-\emph on
-etc
-\emph default
-
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://perldoc.perl.org/perlreref.html"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-.
- If you want to
-\series bold
-grab
-\series default
- records withs the sequence ATCG or GCTA you can do this:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --regex='ATCG|GCTA'
-\end_layout
-
-\begin_layout Standard
-Or if you want to find sequences beginning with ATCG:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --regex='^ATCG'
-\end_layout
-
-\begin_layout Standard
-You can also use
-\series bold
-grab
-\series default
- to locate records that fulfill a numerical property using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-eval switch witch takes an expression in three parts.
- The first part is the key that holds the value we want to evaluate, the
- second part holds one the six operators:
-\end_layout
-
-\begin_layout Enumerate
-Greater than: >
-\end_layout
-
-\begin_layout Enumerate
-Greater than or equal to: >=
-\end_layout
-
-\begin_layout Enumerate
-Less than: <
-\end_layout
-
-\begin_layout Enumerate
-Less than or equal to: <=
-\end_layout
-
-\begin_layout Enumerate
-Equal to: =
-\end_layout
-
-\begin_layout Enumerate
-Not equal to: !=
-\end_layout
-
-\begin_layout Enumerate
-String wise equal to: eq
-\end_layout
-
-\begin_layout Enumerate
-String wise not equal to: ne
-\end_layout
-
-\begin_layout Standard
-And finally comes the number used in the evaluation.
- So to
-\series bold
-grab
-\series default
- all records with a sequence length greater than 30:
-\end_layout
-
-\begin_layout LyX-Code
-...
- length_seq | grab --eval='SEQ_LEN > 30'
-\end_layout
-
-\begin_layout Standard
-If you want to locate all records containing the pattern 'human' and where
- the sequence length is greater that 30, you do this by running the stream
- through
-\series bold
-grab
-\series default
- twice:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern='human' | length_seq | grab --eval='SEQ_LEN > 30'
-\end_layout
-
-\begin_layout Standard
-Finally, it is possible to do fast matching of expressions from a file using
- the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-exact switch.
- Each of these expressions has to be matched exactly over the entrie length,
- which if useful if you have a file with accession numbers, that you want
- to locate in the stream:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --exact acc_no.txt | ...
-\end_layout
-
-\begin_layout Standard
-Using
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-exact is much faster than using
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in, because with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-exact the expression has to be complete matches, where
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in looks for subpatterns.
-\end_layout
-
-\begin_layout Standard
-NB! To get the best speed performance, use the most restrictive
-\series bold
-grab
-\series default
- first.
-\end_layout
-
-\begin_layout Subsection
-How to remove keys from records?
-\end_layout
-
-\begin_layout Standard
-To remove one or more specific keys from all records in the data stream
- use
-\series bold
-remove_keys
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | remove_keys --keys=SEQ,SEQ_NAME
-\end_layout
-
-\begin_layout Standard
-In the above example SEQ and SEQ_NAME will be removed from all records if
- they exists in these.
- If all keys are removed from a record, then the record will be removed.
-\end_layout
-
-\begin_layout Subsection
-How to rename keys in records?
-\end_layout
-
-\begin_layout Standard
-Sometimes you want to rename a record key,
-\emph on
-e.g.
-
-\emph default
- if you have read in a two column table with sequence name and sequence
- in each column (see
-\begin_inset LatexCommand ref
-reference "sub:How-to-read-table"
-
-\end_inset
-
-) without specifying the key names, then the sequence name will be called
- V0 and the sequence V1 as default in the
-\series bold
-read_tab
-\series default
- biotool.
- To rename the V0 and V1 keys we need to run the stream through
-\series bold
-rename_keys
-\series default
- twice (one for each key to rename):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | rename_keys --keys=V0,SEQ_NAME | rename_keys --keys=V1,SEQ
-\end_layout
-
-\begin_layout Standard
-The first instance of
-\series bold
-rename_keys
-\series default
- replaces all the V0 keys with SEQ_NAME, and the second instance of
-\series bold
-rename_keys
-\series default
- replaces all the V1 keys with SEQ.
-
-\emph on
-Et viola
-\emph default
- the data can now be used in the biotools that requires these keys.
-\end_layout
-
-\begin_layout Section
-Manipulating Sequences
-\end_layout
-
-\begin_layout Subsection
-How to get sequence lengths?
-\end_layout
-
-\begin_layout Standard
-The length for sequences in records can be determined with
-\series bold
-length_seq
-\series default
-, which adds the key SEQ_LEN to each record with the sequence length as
- the value.
- It also generates an extra record that is emitted last with the key TOTAL_SEQ_L
-EN showing the total length of all the sequences.
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_seq
-\end_layout
-
-\begin_layout Standard
-It is also possible to determine the sequence length using the generic tool
-
-\series bold
-length_vals
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-get-value_length"
-
-\end_inset
-
-, which determines the length of the values for a given list of keys:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_vals --keys=SEQ
-\end_layout
-
-\begin_layout Standard
-To obtain the total length of all sequences use
-\series bold
-sum_vals
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_vals --keys=SEQ
-\end_layout
-
-\begin_layout LyX-Code
-| sum_vals --keys=SEQ_LEN
-\end_layout
-
-\begin_layout Standard
-The biotool
-\series bold
-analyze_seq
-\series default
- will also determine the length of each sequence (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-analyze"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to analyze sequence composition?
-\begin_inset LatexCommand label
-name "sub:How-to-analyze"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-If you want to find out the sequence type, composition, length, as well
- as GC content, indel content and proportions of soft and hard masked sequence,
- then use
-\series bold
-analyze_seq
-\series default
-.
- This handy biotool will determine all these things per sequence from which
- it is easy to get an overview using the
-\series bold
-write_tab
-\series default
- biotool to output a table (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-tab"
-
-\end_inset
-
-).
- So in order to determine the sequence composition of a FASTA file with
- just one entry containing the sequence 'ATCG' we just read the data with
-
-\series bold
-read_fasta
-\series default
- and run the output through
-\series bold
-analyze_seq
-\series default
- which will add the analysis to the record like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq ...
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:D: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-MIX_INDEX: 0.55
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:W: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:G: 16
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SOFT_MASK%: 63.75
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:B: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:V: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-HARD_MASK%: 0.00
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:H: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:S: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:N: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:.: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-GC%: 35.00
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:A: 8
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:Y: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:M: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:T: 44
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SEQ_TYPE: DNA
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:K: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:~: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SEQ: TTTCAGTTTGGGACGGAGTAAGGCCTTCCtttttttttttttttttttttttttttttgagaccgagtcttgctc
-tgtcg
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SEQ_LEN:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-80 RES:R: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:C: 12
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:-: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:U: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
----
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout Standard
-Now to make a table of how may As, Ts, Cs, and Gs you can add the following:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | analyze_seq | write_tab --keys=RES:A,RES:T,RES:C,RES:G
-\end_layout
-
-\begin_layout Standard
-Or if you want to see the proportions of hard and soft masked sequence:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | analyse_seq | write_tab --keys=HARD_MASK%,SOFT_MASK%
-\end_layout
-
-\begin_layout Standard
-If you have a stack of sequences in one file and you want to determine the
- mean GC content you can do it using the
-\series bold
-mean_vals
-\series default
- biotool:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq | mean_vals --keys=GC%
-\end_layout
-
-\begin_layout Standard
-Or if you want the total count of Ns you can use
-\series bold
-sum_vals
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq | sum_vals --keys=RES:N
-\end_layout
-
-\begin_layout Standard
-The MIX_INDEX key is calculated as the count of the most common residue
- over the sequence length, and can be used as a cut-off for removing sequence
- tags consisting of mostly one nucleotide:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq | grab --eval='MIX_INDEX<0.85'
-\end_layout
-
-\begin_layout Subsection
-How to extract subsequences?
-\begin_inset LatexCommand label
-name "sub:How-to-extract"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-In order to extract a subsequence from a longer sequence use the biotool
- extract_seq, which will replace the sequence in the record with the subsequence
- (this behaviour should probably be modified to be dependant of a
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-replace or a
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_replace switch
-\begin_inset Note Note
-status collapsed
-
-\begin_layout Standard
-also in split_seq
-\end_layout
-
-\end_inset
-
-).
- So to extract the first 20 residues from all sequences do (first residue
- is designated 1):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | extract_seq --beg=1 --len=20
-\end_layout
-
-\begin_layout Standard
-You can also specify a begin and end coordinate set:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | extract_seq --beg=20 --end=40
-\end_layout
-
-\begin_layout Standard
-If you want the subsequences from position 20 to the sequence end do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | extract_seq --beg=20
-\end_layout
-
-\begin_layout Standard
-If you want to extract subsequences a given distance from the sequence end
- you can do this by reversing the sequence with the biotool
-\series bold
-reverse_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-reverse-seq"
-
-\end_inset
-
-, followed by
-\series bold
-extract_seq
-\series default
- to get the subsequence, and then
-\series bold
-reverse_seq
-\series default
- again to get the subsequence back in the original orientation:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | reverse_seq
-\end_layout
-
-\begin_layout LyX-Code
-| extract_seq --beg=10 --len=10 | reverse_seq
-\end_layout
-
-\begin_layout Subsection
-How to get genomic sequence?
-\begin_inset LatexCommand label
-name "sub:How-to-get-genomic-sequence"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The biotool
-\series bold
-get_genomic_seq
-\series default
- can extract subsequences for a given genome specified with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-genome switch explicitly using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-beg and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-end/
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-len switches:
-\end_layout
-
-\begin_layout LyX-Code
-get_genome_seq --genome=<genome> --beg=1 --len=100
-\end_layout
-
-\begin_layout Standard
-Alternatively,
-\series bold
-get_genome_seq
-\series default
- can be used to append the corresponding sequence to BED, PSL, and BLAST
- records:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<BED file> | get_genome_seq --genome=<genome>
-\end_layout
-
-\begin_layout Standard
-It is also possible to include flaking sequence using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-flank switch.
- So to include 50 nucleotides upstream and 50 nucleotides downstream for
- each BED entry do:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<BED file> | get_genome_seq --genome=<genome> --flank=50
-\end_layout
-
-\begin_layout Subsection
-How to upper-case sequences?
-\end_layout
-
-\begin_layout Standard
-Sequences can be shifted from lower case to upper case using
-\series bold
-uppercase_seq
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | uppercase_seq
-\end_layout
-
-\begin_layout Subsection
-How to reverse sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-reverse-seq"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The order of residues in a sequence can be reversed using reverse_seq:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | reverse_seq
-\end_layout
-
-\begin_layout Standard
-Note that in order to reverse/complement a sequence you also need the
-\series bold
-complement_seq
-\series default
- biotool (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-complement"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to complement sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-complement"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-DNA and RNA sequences can be complemented with
-\series bold
-complement_seq
-\series default
-, which automagically determines the sequence type:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | complement_seq
-\end_layout
-
-\begin_layout Standard
-Note that in order to reverse/complement a sequence you also need the
-\series bold
-reverse_seq
-\series default
- biotool (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-reverse-seq"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to remove indels from sequnces?
-\end_layout
-
-\begin_layout Standard
-Indels can be removed from sequences with the
-\series bold
-remove_indels
-\series default
- biotool.
- This is useful if you have aligned some sequences (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-align"
-
-\end_inset
-
-) and extracted (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-extract"
-
-\end_inset
-
-) a block of subsequences from the alignment and you want to use these sequence
- in a search where you need to remove the indels first.
- '-', '~', and '.' are considered indels:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | remove_indels
-\end_layout
-
-\begin_layout Subsection
-How to shuffle sequences?
-\end_layout
-
-\begin_layout Standard
-All residues in sequences in the stream can be shuffled to random positions
- using the
-\series bold
-shuffle_seq
-\series default
- biotool:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | shuffle_seq
-\end_layout
-
-\begin_layout Subsection
-How to split sequences into overlapping subsequences?
-\end_layout
-
-\begin_layout Standard
-Sequences can be slit into overlapping subsequences with the
-\series bold
-split_seq
-\series default
- biotool.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | split_seq --word_size=20 --uniq
-\end_layout
-
-\begin_layout Subsection
-How to determine the oligo frequency?
-\end_layout
-
-\begin_layout Standard
-In order to determine if any oligo usage is over represented in one or more
- sequences you can determine the frequency of oligos of a given size with
-
-\series bold
-oligo_freq
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | oligo_freq --word_size=4
-\end_layout
-
-\begin_layout Standard
-And if you have more than one sequence and want to accumulate the frequences
- you need the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-all switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | oligo_freq --word_size=4 --all
-\end_layout
-
-\begin_layout Standard
-To get a meaningful result you need to write the resulting frequencies as
- a table with
-\series bold
-write_tab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-tab"
-
-\end_inset
-
-), but first it is important to
-\series bold
-grab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-grab"
-
-\end_inset
-
-) the records with the frequencies to avoid full length sequences in the
- table:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | oligo_freq --word_size=4 --all | grab --pattern=OLIGO --keys_only
-\end_layout
-
-\begin_layout LyX-Code
-| write_tab --no_stream
-\end_layout
-
-\begin_layout Standard
-And the resulting frequency table can be sorted with Unix sort (man sort).
-\end_layout
-
-\begin_layout Subsection
-How to search for sequences in genomes?
-\end_layout
-
-\begin_layout Standard
-See the following biotool:
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-patscan_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-patscan"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-blat_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAT"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-blast_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAST"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-vmatch_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-Vmatch"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to search sequences for a pattern?
-\begin_inset LatexCommand label
-name "sub:How-to-use-patscan"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-It is possible to search sequences in the data stream for patterns using
- the
-\series bold
-patscan_seq
-\series default
- biotool which utilizes the powerful scan_for_matches engine.
- Consult the documentation for scan_for_matches in order to learn how to
- define patterns (the documentation is included in Appendix\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sec:scan_for_matches-README"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Standard
-To search all sequences for a simple pattern consisting of the sequence
- ATCGATCG allowing for 3 mismatches, 2 insertions and 1 deletion:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | patscan_seq --pattern='ATCGATCG[3,2,1]'
-\end_layout
-
-\begin_layout Standard
-The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern switch takes a comma seperated list of patterns, so if you want
- to search for more that one pattern do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern='ATCGATCG[3,2,1],GCTAGCTA[3,2,1]'
-\end_layout
-
-\begin_layout Standard
-It is also possible to have a list of different patterns to search for in
- a file with one pattern per line.
- In order to get
-\series bold
-patscan_seq
-\series default
- to read these patterns use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern_in=<file>
-\end_layout
-
-\begin_layout Standard
-To also scan the complementary strand in nucleotide sequences (
-\series bold
-patscan_seq
-\series default
- automagically determines the sequence type) you need to add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-comp switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern=<pattern> --comp
-\end_layout
-
-\begin_layout Standard
-It is also possible to use
-\series bold
-patscan_seq
-\series default
- to output those records that does not contain a certain pattern by using
- the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-invert switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern=<pattern> --invert
-\end_layout
-
-\begin_layout Standard
-Finally,
-\series bold
-patscan_seq
-\series default
- can also scan for patterns in a given genome sequence, instead of sequences
- in the stream, using the
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-genome switch:
-\end_layout
-
-\begin_layout LyX-Code
-patscan --pattern=<pattern> --genome=<genome>
-\end_layout
-
-\begin_layout Subsection
-How to use BLAT for sequence search?
-\begin_inset LatexCommand label
-name "sub:How-to-use-BLAT"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Sequences in the data stream can be matched against supported genomes using
-
-\series bold
-blat_seq
-\series default
- which is a biotool using BLAT as the name might suggest.
- Currently only Mouse and Human genomes are available and it is not possible
- to use OOC files since there is still a need for a local repository for
- genome files.
- Otherwise it is just:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | blat_seq --genome=<genome>
-\end_layout
-
-\begin_layout Standard
-The search results can then be written to file with
-\series bold
-write_psl
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-PSL"
-
-\end_inset
-
-) or
-\series bold
-write_bed
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-BED"
-
-\end_inset
-
-) allthough with
-\series bold
-write_bed
-\series default
- some information will be lost).
- It is also possible to plot chromosome distribution of the search results
- using
-\series bold
-plot_chrdist
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-plot-chrdist"
-
-\end_inset
-
-) or the distribution of the match lengths using
-\series bold
-plot_lendist
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-plot-lendist"
-
-\end_inset
-
-) or a karyogram with the hits using
-\series bold
-plot_karyogram
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-plot-karyogram"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to use BLAST for sequence search?
-\begin_inset LatexCommand label
-name "sub:How-to-use-BLAST"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Two biotools exist for blasting sequences:
-\series bold
-create_blast_db
-\series default
- is used to create the BLAST database required for BLAST which is queried
- using the biotool
-\series bold
-blast_seq
-\series default
-.
- So in order to create a BLAST database from sequences in the data stream
- you simple run:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_blast_db --database=my_database --no_stream
-\end_layout
-
-\begin_layout Standard
-The type of sequence to use for the database is automagically determined
- by
-\series bold
-create_blast_db
-\series default
-, but don't have a mixture of peptide and nucleic acids sequences in the
- stream.
- The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-database switch takes a path as argument, but will default to 'blastdb_<time_sta
-mp> if not set.
-\end_layout
-
-\begin_layout Standard
-The resulting database can now be queried with sequences in another data
- stream using
-\series bold
-blast_seq
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | blast_seq --database=my_database
-\end_layout
-
-\begin_layout Standard
-Again, the sequence type is determined automagically and the appropriate
- BLAST program is guessed (see below table), however, the program name can
- be overruled with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-program switch.
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Tabular
-<lyxtabular version="3" rows="5" columns="3">
-<features>
-<column alignment="center" valignment="top" width="0">
-<column alignment="center" valignment="top" width="0">
-<column alignment="center" valignment="top" width="0">
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Subject sequence
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Query sequence
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Program guess
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-blastn
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-blastp
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-blastx
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-tblastn
-\end_layout
-
-\end_inset
-</cell>
-</row>
-</lyxtabular>
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Finally, it is also possible to use
-\series bold
-blast_seq
-\series default
- for blasting sequences agains a preformatted genome using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-genome switch instead of the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-database switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | blast_seq --genome=<genome>
-\end_layout
-
-\begin_layout Subsection
-How to use Vmatch for sequence search?
-\begin_inset LatexCommand label
-name "sub:How-to-use-Vmatch"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The powerful suffix array software package Vmatch
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://www.vmatch.de/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
- can be used for exact mapping of sequences against indexed genomes using
- the biotool
-\series bold
-vmatch_seq
-\series default
-, which will e.g.
- map 700000 ESTs to the human genome locating all 160 mio hits in less than
- an hour.
- Only nucleotide sequences and sequences longer than 11 nucleotides will
- be mapped.
- It is recommended that sequences consisting of mostly one nucleotide type
- are removed.
- This can be done with the
-\series bold
-analyze_seq
-\series default
- biotool
-\begin_inset LatexCommand eqref
-reference "sub:How-to-analyze"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome>
-\end_layout
-
-\begin_layout Standard
-It is also possible to allow for mismatches using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-hamming_dist switch.
- So to allow for 2 mismatches:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=2
-\end_layout
-
-\begin_layout Standard
-Or to allow for 10% mismathing nucleotides:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=10p
-\end_layout
-
-\begin_layout Standard
-To allow both indels and mismatches use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-edit_dist switch.
- So to allow for one mismatch or one indel:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=1
-\end_layout
-
-\begin_layout Standard
-Or to allow for 5% indels or mismatches:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=5p
-\end_layout
-
-\begin_layout Standard
-Note that using
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-hamming_dist or
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-edit_dist greatly slows down vmatch considerably --- use with care.
-\end_layout
-
-\begin_layout Standard
-The resulting SCORE key can be replaced to hold the number of genome matches
- of a given sequence (multi-mappers) is the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-count switch is given.
-\end_layout
-
-\begin_layout Subsection
-How to find all matches between sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-find-matches"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-All matches between two sequences can be determined with the biotool
-\series bold
-match_seq
-\series default
-.
- The match finding engine underneath the hood of
-\series bold
-match_seq
-\series default
- is the super fast suffix tree program MUMmer
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://mummer.sourceforge.net/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-, which will locate all forward and reverse matches between huge sequences
- in a matter of minutes (if the repeat count is not too high and if the
- word size used is appropriate).
- Matching two
-\emph on
-Helicobacter pylori
-\emph default
- genomes (1.7Mbp) takes around 10 seconds:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | match_seq --word_size=20 --direction=both
-\end_layout
-
-\begin_layout Standard
-The output from
-\series bold
-match_seq
-\series default
- can be used to generate a dot plot with
-\series bold
-plot_matches
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-generate-dotplot"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to align sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-align"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Sequences in the stream can be aligned with the
-\series bold
-align_seq
-\series default
- biotool that uses Muscle
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://www.drive5.com/muscle/muscle.html"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
- as aligment engine.
- Currently you cannot change any of the Muscle alignment parameters and
-
-\series bold
-align_seq
-\series default
- will create an alignment based on the defaults (which are really good!):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | align_seq
-\end_layout
-
-\begin_layout Standard
-The aligned output can be written to file in FASTA format using
-\series bold
-write_fasta
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-fasta"
-
-\end_inset
-
-) or in pretty text using
-\series bold
-write_align
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-alignment"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to create a weight matrix?
-\end_layout
-
-\begin_layout Standard
-If you want a weight matrix to show the sequence composition of a stack
- of sequences you can use the biotool create_weight_matrix:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_weight_matrix
-\end_layout
-
-\begin_layout Standard
-The result can be output in percent using the
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-percent switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_weight_matrix --percent
-\end_layout
-
-\begin_layout Standard
-The weight matrix can be written as tabular output with
-\series bold
-write_tab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-tab"
-
-\end_inset
-
-) after removeing the records containing SEQ with
-\series bold
-grab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-grab"
-
-\end_inset
-
-):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_weight_matrix | grab --invert --keys=SEQ --keys_only
-\end_layout
-
-\begin_layout LyX-Code
-| write_tab --no_stream
-\end_layout
-
-\begin_layout Standard
-The V0 column will hold the residue, while the rest of the columns will
- hold the frequencies for each sequence position.
-\end_layout
-
-\begin_layout Section
-Plotting
-\end_layout
-
-\begin_layout Standard
-There exists several biotools for plotting.
- Some of these are based on GNUplot
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://www.gnuplot.info/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-, which is an extremely powerful platform to generate all sorts of plots
- and even though GNUplot has quite a steep learning curve, the biotools
- utilizing GNUplot are simple to use.
- GNUplot is able to output a lot of different formats (called terminals
- in GNUplot), but the biotools focusses on three formats only:
-\end_layout
-
-\begin_layout Enumerate
-The 'dumb' terminal is default to the GNUplot based biotools and will output
- a plot in crude ASCII text (Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Dumb-terminal"
-
-\end_inset
-
-).
- This is quite nice for a quick and dirty plot to get an overview of your
- data .
-\end_layout
-
-\begin_layout Enumerate
-The 'post' or 'postscript' terminal output postscript code which is publication
- grade graphics that can be viewed with applications such as Ghostview,
- Photoshop, and Preview.
-\end_layout
-
-\begin_layout Enumerate
-The 'svg' terminal output's scalable vector graphics (SVG) which is a vector
- based format.
- SVG is great because you can edit the resulting plot using Photoshop or
- Inkscape
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-Inkscape is a really handy drawing program that is free and open source.
- Availble at
-\begin_inset LatexCommand htmlurl
-target "http://www.inkscape.org"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
- if you want to add additional labels, captions, arrows, and so on and then
- save the result in different formats, such as postscript without loosing
- resolution.
-\end_layout
-
-\begin_layout Standard
-The biotools for plotting that are not based on GNUplot only output SVG
- (that may change in the future).
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename lendist_ascii.png
- lyxscale 70
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Dumb-terminal"
-
-\end_inset
-
-Dumb terminal
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-The output of a length distribution plot in the default 'dumb terminal'
- to the terminal window.
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a histogram?
-\begin_inset LatexCommand label
-name "How-to-plot-histogram"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-A generic histogram for a given value can be plotted with the biotool
-\series bold
-plot_histogram
-\series default
- (Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Histogram"
-
-\end_inset
-
-):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_histogram --key=TISSUE --no_stream
-\end_layout
-
-\begin_layout Standard
-(Figure missing)
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align left
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename histogram.png
- lyxscale 70
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Histogram"
-
-\end_inset
-
-Histogram
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a length distribution?
-\begin_inset LatexCommand label
-name "sub:How-to-plot-lendist"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Plotting of length distributions, weather sequence lengths, patterns lengths,
- hit lengths,
-\emph on
-etc.
-
-\emph default
- is a really handy thing and can be done with the the biotool
-\series bold
-plot_lendist
-\series default
-.
- If you have a file with FASTA entries and want to plot the length distribution
- you do it like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_seq
-\end_layout
-
-\begin_layout LyX-Code
-| plot_lendist --key=SEQ_LEN --no_stream
-\end_layout
-
-\begin_layout Standard
-The result will be written to the default dumb terminal and will look like
- Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Dumb-terminal"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-If you instead want the result in postscript format you can do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_lendist --key=SEQ_LEN --terminal=post --result_out=file.ps
-\end_layout
-
-\begin_layout Standard
-That will generate the plot and save it to file, but not interrupt the data
- stream which can then be used in further analysis.
- You can also save the plot implicetly using '>', however, it is then important
- to terminate the stream with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_lendist --key=SEQ_LEN --terminal=post --no_stream > file.ps
-\end_layout
-
-\begin_layout Standard
-The resulting plot can be seen in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Length-distribution"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename lendist.ps
- lyxscale 50
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Length-distribution"
-
-\end_inset
-
-Length distribution
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-Length distribution of 630 piRNA like RNAs.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a chromosome distribution?
-\begin_inset LatexCommand label
-name "sub:How-to-plot-chrdist"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-If you have the result of a sequence search against a multi chromosome genome,
- it is very practical to be able to plot the distribution of search hits
- on the different chromosomes.
- This can be done with
-\series bold
-plot_chrdist
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | blat_genome | plot_chrdist --no_stream
-\end_layout
-
-\begin_layout Standard
-The above example will result in a crude plot using the 'dumb' terminal,
- and if you want to mess around with the results from the BLAT search you
- probably want to save the result to file first (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-PSL"
-
-\end_inset
-
-).
- To plot the chromosome distribution from the saved search result you can
- do:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=file.bed | plot_chrdist --terminal=post --result_out=plot.ps
-\end_layout
-
-\begin_layout Standard
-That will result in the output show in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Chromosome-distribution"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename chrdist.ps
- lyxscale 50
- width 12cm
- rotateAngle 90
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Chromosome-distribution"
-
-\end_inset
-
-Chromosome distribution
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to generate a dotplot?
-\begin_inset LatexCommand label
-name "sub:How-to-generate-dotplot"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-A dotplot is a powerful way to get an overview of the size and location
- of sequence insertions, deletions, and duplications between two sequences.
- Generating a dotplot with biotools is a two step process where you initially
- find all matches between two sequences using the tool
-\series bold
-match_seq
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-find-matches"
-
-\end_inset
-
-) and plot the resulting matches with
-\series bold
-plot_matches
-\series default
-.
- Matching and plotting two
-\emph on
-Helicobacter pylori
-\emph default
- genomes (1.7Mbp) takes around 10 seconds:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | match_seq | plot_matches --terminal=post --result_out=plot.ps
-\end_layout
-
-\begin_layout Standard
-The resulting dotplot is in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Dotplot"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename dotplot.ps
- lyxscale 50
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Dotplot"
-
-\end_inset
-
-Dotplot
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-Forward matches are displayed in green while reverse matches are displayed
- in red.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a sequence logo?
-\end_layout
-
-\begin_layout Standard
-Sequence logos can be generate with
-\series bold
-plot_seqlogo
-\series default
-.
- The sequnce type is determined automagically and an entropy scale of 2
- bits and 4 bits is used for nucleotide and peptide sequences, respectively
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand htmlurl
-target "http://www.ccrnp.ncifcrf.gov/~toms/paper/hawaii/latex/node5.html"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_seqlogo --no_stream --result_out=seqlogo.svg
-\end_layout
-
-\begin_layout Standard
-An example of a sequence logo can be seen in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Sequence-logo"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename seqlogo.png
- lyxscale 50
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Sequence-logo"
-
-\end_inset
-
-Sequence logo
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a karyogram?
-\begin_inset LatexCommand label
-name "sub:How-to-plot-karyogram"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-To plot search hits on genomes use
-\series bold
-plot_karyogram
-\series default
-, which will output a nice karyogram in SVG graphics:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_karyogram --result_out=karyogram.svg
-\end_layout
-
-\begin_layout Standard
-The banding data is taken from the UCSC genome browser database and currently
- only Human and Mouse is supported.
- Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Karyogram"
-
-\end_inset
-
- shows the distribution of piRNA like RNAs matched to the Human genome.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename karyogram.png
- lyxscale 35
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Karyogram"
-
-\end_inset
-
-Karyogram
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-Hits from a search of piRNA like RNAs in the Human genome is displayed as
- short horizontal bars.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Section
-Uploading Results
-\end_layout
-
-\begin_layout Subsection
-How do I display my results in the UCSC Genome Browser?
-\end_layout
-
-\begin_layout Standard
-Results from the list of biotools below can be uploaded directly to a local
- mirror of the UCSC Genome Browser using the biotool
-\series bold
-upload_to_ucsc
-\series default
-:
-\end_layout
-
-\begin_layout Itemize
-patscan_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-patscan"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-blat_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAT"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-blast_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAST"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-vmatch_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-Vmatch"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The syntax for uploading data the most simple way requires two mandatory
- switches:
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-database, which is the UCSC database name (such as hg18, mm9, etc.) and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-table which should be the users initials followed by an underscore and a
- short description of the data:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | upload_to_ucsc --database=hg18 --table=mah_snoRNAs
-\end_layout
-
-\begin_layout Standard
-The
-\series bold
-upload_to_ucsc
-\series default
- biotool modifies the users ~/ucsc/my_tracks.ra file automagically (a backup
- is created with the name ~/ucsc/my_tracks.ra~) with default values that
- can be overridden using the following switches:
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-short_label - Short label for track - Default=database->table
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-long_label - Long label for track - Default=database->table
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-group - Track group name - Default=<user name as defined in env>
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-priority - Track display priority - Default=1
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-color - Track color - Default=147,73,42
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-chunk_size - Chunks for loading - Default=10000000
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-visibility - Track visibility - Default=pack
-\end_layout
-
-\begin_layout Standard
-Also, data in BED or PSL format can be uploaded with
-\series bold
-upload_to_ucsc
-\series default
- as long as these reference to genomes and chromosomes existing in the UCSC
- Genome Browser:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<bed file> | upload_to_ucsc ...
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-read_psl --data_in=<psl file> | upload_to_ucsc ...
-\end_layout
-
-\begin_layout Section
-Power Scripting
-\end_layout
-
-\begin_layout Standard
-It is possible to do commandline scripting of biotool records using Perl.
- Because a biotool record essentially is a hash structure, you can pass
- records to
-\series bold
-bioscript
-\series default
- command, which is a wrapper around the Perl executable that allows direct
- manipulations of the records using the power of Perl.
-\end_layout
-
-\begin_layout Standard
-In the below example we replace in all records the value to the CHR key
- with a forthrunning number:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | bioscript 'while($r=get_record(
-\backslash
-*STDIN)){$r->{CHR}=$i++; put_record($r)}'
-\end_layout
-
-\begin_layout Standard
-Something more useful would probably be to create custom FASTA headers.
- E.g.
- if we read in a BED file, lookup the genomic sequence, create a custom
- FASTA header with
-\series bold
-bioscript
-\series default
- and output FASTA entries:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | bioscript 'while($r=get_record(
-\backslash
-*STDIN)){$r->{SEQ_NAME}= //
-\end_layout
-
-\begin_layout LyX-Code
-join("_",$r->{CHR},$r->{CHR_BEG},$r->{CHR_END}); put_record($r)}'
-\end_layout
-
-\begin_layout Standard
-And the output:
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_21567527_21567550
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_693380_693403
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_13859534_13859557
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_9005090_9005113
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_2106825_2106848
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_14649031_14649054
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout Section
-Trouble shooting
-\end_layout
-
-\begin_layout Standard
-Shoot the messenger!
-\end_layout
-
-\begin_layout Section
-\start_of_appendix
-Keys
-\begin_inset LatexCommand label
-name "sec:Keys"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-HIT
-\end_layout
-
-\begin_layout Standard
-HIT_BEG
-\end_layout
-
-\begin_layout Standard
-HIT_END
-\end_layout
-
-\begin_layout Standard
-HIT_LEN
-\end_layout
-
-\begin_layout Standard
-HIT_NAME
-\end_layout
-
-\begin_layout Standard
-PATTERN
-\end_layout
-
-\begin_layout Section
-Switches
-\begin_inset LatexCommand label
-name "sec:Switches"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_in
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_out
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-data_in
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num
-\end_layout
-
-\begin_layout Section
-scan_for_matches README
-\begin_inset LatexCommand label
-name "sec:scan_for_matches-README"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches:
-\end_layout
-
-\begin_layout LyX-Code
- A Program to Scan Nucleotide or Protein Sequences for Matching Patterns
-\end_layout
-
-\begin_layout LyX-Code
- Ross Overbeek
-\end_layout
-
-\begin_layout LyX-Code
- MCS
-\end_layout
-
-\begin_layout LyX-Code
- Argonne National Laboratory
-\end_layout
-
-\begin_layout LyX-Code
- Argonne, IL 60439
-\end_layout
-
-\begin_layout LyX-Code
- USA
-\end_layout
-
-\begin_layout LyX-Code
-Scan_for_matches is a utility that we have written to search for
-\end_layout
-
-\begin_layout LyX-Code
-patterns in DNA and protein sequences.
- I wrote most of the code,
-\end_layout
-
-\begin_layout LyX-Code
-although David Joerg and Morgan Price wrote sections of an
-\end_layout
-
-\begin_layout LyX-Code
-earlier version.
- The whole notion of pattern matching has a rich
-\end_layout
-
-\begin_layout LyX-Code
-history, and we borrowed liberally from many sources.
- However, it is
-\end_layout
-
-\begin_layout LyX-Code
-worth noting that we were strongly influenced by the elegant tools
-\end_layout
-
-\begin_layout LyX-Code
-developed and distributed by David Searls.
- My intent is to make the
-\end_layout
-
-\begin_layout LyX-Code
-existing tool available to anyone in the research community that might
-\end_layout
-
-\begin_layout LyX-Code
-find it useful.
- I will continue to try to fix bugs and make suggested
-\end_layout
-
-\begin_layout LyX-Code
-enhancements, at least until I feel that a superior tool exists.
-\end_layout
-
-\begin_layout LyX-Code
-Hence, I would appreciate it if all bug reports and suggestions are
-\end_layout
-
-\begin_layout LyX-Code
-directed to me at Overbeek@mcs.anl.gov.
-
-\end_layout
-
-\begin_layout LyX-Code
-I will try to log all bug fixes and report them to users that send me
-\end_layout
-
-\begin_layout LyX-Code
-their email addresses.
- I do not require that you give me your name
-\end_layout
-
-\begin_layout LyX-Code
-and address.
- However, if you do give it to me, I will try to notify
-\end_layout
-
-\begin_layout LyX-Code
-you of serious problems as they are discovered.
-\end_layout
-
-\begin_layout LyX-Code
-Getting Started:
-\end_layout
-
-\begin_layout LyX-Code
- The distribution should contain at least the following programs:
-\end_layout
-
-\begin_layout LyX-Code
- README - This document
-\end_layout
-
-\begin_layout LyX-Code
- ggpunit.c - One of the two source files
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches.c - The second source file
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- run_tests - A perl script to test things
-\end_layout
-
-\begin_layout LyX-Code
- show_hits - A handy perl script
-\end_layout
-
-\begin_layout LyX-Code
- test_dna_input - Test sequences for DNA
-\end_layout
-
-\begin_layout LyX-Code
- test_dna_patterns - Test patterns for DNA scan
-\end_layout
-
-\begin_layout LyX-Code
- test_output - Desired output from test
-\end_layout
-
-\begin_layout LyX-Code
- test_prot_input - Test protein sequences
-\end_layout
-
-\begin_layout LyX-Code
- test_prot_patterns - Test patterns for proteins
-\end_layout
-
-\begin_layout LyX-Code
- testit - a perl script used for test
-\end_layout
-
-\begin_layout LyX-Code
- Only the first three files are required.
- The others are useful,
-\end_layout
-
-\begin_layout LyX-Code
- but only if you have Perl installed on your system.
- If you do
-\end_layout
-
-\begin_layout LyX-Code
- have Perl, I suggest that you type
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- which perl
-\end_layout
-
-\begin_layout LyX-Code
- to find out where it installed.
- On my system, I get the following
-\end_layout
-
-\begin_layout LyX-Code
- response:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- clone% which perl
-\end_layout
-
-\begin_layout LyX-Code
- /usr/local/bin/perl
-\end_layout
-
-\begin_layout LyX-Code
- indicating that Perl is installed in /usr/local/bin.
- Anyway, once
-\end_layout
-
-\begin_layout LyX-Code
- you know where it is installed, edit the first line of files
-\end_layout
-
-\begin_layout LyX-Code
- testit
-\end_layout
-
-\begin_layout LyX-Code
- show_hits
-\end_layout
-
-\begin_layout LyX-Code
- replacing /usr/local/bin/perl with the appropriate location.
- I
-\end_layout
-
-\begin_layout LyX-Code
- will assume that you can do this, although it is not critical (it
-\end_layout
-
-\begin_layout LyX-Code
- is needed only to test the installation and to use the "show_hits"
-\end_layout
-
-\begin_layout LyX-Code
- utility).
- Perl is not required to actually install and run
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches.
-
-\end_layout
-
-\begin_layout LyX-Code
- If you do not have Perl, I suggest you get it and install it (it
-\end_layout
-
-\begin_layout LyX-Code
- is a wonderful utility).
- Information about Perl and how to get it
-\end_layout
-
-\begin_layout LyX-Code
- can be found in the book "Programming Perl" by Larry Wall and
-\end_layout
-
-\begin_layout LyX-Code
- Randall L.
- Schwartz, published by O'Reilly & Associates, Inc.
-\end_layout
-
-\begin_layout LyX-Code
- To get started, you will need to compile the program.
- I do this
-\end_layout
-
-\begin_layout LyX-Code
- using
-\end_layout
-
-\begin_layout LyX-Code
- gcc -O -o scan_for_matches ggpunit.c scan_for_matches.c
-\end_layout
-
-\begin_layout LyX-Code
- If you do not use GNU C, use
-\end_layout
-
-\begin_layout LyX-Code
- cc -O -DCC -o scan_for_matches ggpunit.c scan_for_matches.c
-\end_layout
-
-\begin_layout LyX-Code
- which works on my Sun.
-
-\end_layout
-
-\begin_layout LyX-Code
- Once you have compiled scan_for_matches, you can verify that it
-\end_layout
-
-\begin_layout LyX-Code
- works with
-\end_layout
-
-\begin_layout LyX-Code
- clone% run_tests tmp
-\end_layout
-
-\begin_layout LyX-Code
- clone% diff tmp test_output
-\end_layout
-
-\begin_layout LyX-Code
- You may get a few strange lines of the sort
-\end_layout
-
-\begin_layout LyX-Code
- clone% run_tests tmp
-\end_layout
-
-\begin_layout LyX-Code
- rm: tmp: No such file or directory
-\end_layout
-
-\begin_layout LyX-Code
- clone% diff tmp test_output
-\end_layout
-
-\begin_layout LyX-Code
- These should cause no concern.
- However, if the "diff" shows that
-\end_layout
-
-\begin_layout LyX-Code
- tmp and test_output are different, contact me (you have a
-\end_layout
-
-\begin_layout LyX-Code
- problem).
-
-\end_layout
-
-\begin_layout LyX-Code
- You should now be able to use scan_for_matches by following the
-\end_layout
-
-\begin_layout LyX-Code
- instructions given below (which is all the normal user should have
-\end_layout
-
-\begin_layout LyX-Code
- to understand, once things are installed properly).
-\end_layout
-
-\begin_layout LyX-Code
- ==============================================================
-\end_layout
-
-\begin_layout LyX-Code
-How to run scan_for_matches:
-\end_layout
-
-\begin_layout LyX-Code
- To run the program, you type need to create two files
-\end_layout
-
-\begin_layout LyX-Code
- 1.
- the first file contains the pattern you wish to scan for; I'll
-\end_layout
-
-\begin_layout LyX-Code
- call this file pat_file in what follows (but any name is ok)
-\end_layout
-
-\begin_layout LyX-Code
- 2.
- the second file contains a set of sequences to scan.
- These
-\end_layout
-
-\begin_layout LyX-Code
- should be in "fasta format".
- Just look at the contents of
-\end_layout
-
-\begin_layout LyX-Code
- test_dna_input to see examples of this format.
- Basically,
-\end_layout
-
-\begin_layout LyX-Code
- each sequence begins with a line of the form
-\end_layout
-
-\begin_layout LyX-Code
- >sequence_id
-\end_layout
-
-\begin_layout LyX-Code
- and is followed by one or more lines containing the sequence.
-\end_layout
-
-\begin_layout LyX-Code
- Once these files have been created, you just use
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches pat_file < input_file
-\end_layout
-
-\begin_layout LyX-Code
- to scan all of the input sequences for the given pattern.
- As an
-\end_layout
-
-\begin_layout LyX-Code
- example, suppose that pat_file contains a single line of the form
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...7 3...8 ~p1
-\end_layout
-
-\begin_layout LyX-Code
- Then,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- should produce two "hits".
- When I run this on my machine, I get
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[6,27]
-\end_layout
-
-\begin_layout LyX-Code
- cguaacc ggttaacc gguuacg
-\end_layout
-
-\begin_layout LyX-Code
- >tst2:[6,27]
-\end_layout
-
-\begin_layout LyX-Code
- CGUAACC GGTTAACC GGUUACG
-\end_layout
-
-\begin_layout LyX-Code
- clone%
-\end_layout
-
-\begin_layout LyX-Code
-Simple Patterns Built by Matching Ranges and Reverse Complements
-\end_layout
-
-\begin_layout LyX-Code
- Let me first explain this simple pattern:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...7 3...8 ~p1
-\end_layout
-
-\begin_layout LyX-Code
- The pattern consists of three "pattern units" separated by spaces.
-\end_layout
-
-\begin_layout LyX-Code
- The first pattern unit is
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...7
-\end_layout
-
-\begin_layout LyX-Code
- which means "match 4 to 7 characters and call them p1".
- The
-\end_layout
-
-\begin_layout LyX-Code
- second pattern unit is
-\end_layout
-
-\begin_layout LyX-Code
- 3...8
-\end_layout
-
-\begin_layout LyX-Code
- which means "then match 3 to 8 characters".
- The last pattern unit
-\end_layout
-
-\begin_layout LyX-Code
- is
-\end_layout
-
-\begin_layout LyX-Code
- ~p1
-\end_layout
-
-\begin_layout LyX-Code
- which means "match the reverse complement of p1".
- The first
-\end_layout
-
-\begin_layout LyX-Code
- reported hit is shown as
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[6,27]
-\end_layout
-
-\begin_layout LyX-Code
- cguaacc ggttaacc gguuacg
-\end_layout
-
-\begin_layout LyX-Code
- which states that characters 6 through 27 of sequence tst1 were
-\end_layout
-
-\begin_layout LyX-Code
- matched.
- "cguaac" matched the first pattern unit, "ggttaacc" the
-\end_layout
-
-\begin_layout LyX-Code
- second, and "gguuacg" the third.
- This is an example of a common
-\end_layout
-
-\begin_layout LyX-Code
- type of pattern used to search for sections of DNA or RNA that
-\end_layout
-
-\begin_layout LyX-Code
- would fold into a hairpin loop.
-\end_layout
-
-\begin_layout LyX-Code
-Searching Both Strands
-\end_layout
-
-\begin_layout LyX-Code
- Now for a short aside: scan_for_matches only searched the
-\end_layout
-
-\begin_layout LyX-Code
- sequences in the input file; it did not search the opposite
-\end_layout
-
-\begin_layout LyX-Code
- strand.
- With a pattern of the sort we just used, there is not
-\end_layout
-
-\begin_layout LyX-Code
- need o search the opposite strand.
- However, it is normally the
-\end_layout
-
-\begin_layout LyX-Code
- case that you will wish to search both the sequence and the
-\end_layout
-
-\begin_layout LyX-Code
- opposite strand (i.e., the reverse complement of the sequence).
-\end_layout
-
-\begin_layout LyX-Code
- To do that, you would just use the "-c" command line.
- For example,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches -c pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- Hits on the opposite strand will show a beginning location greater
-\end_layout
-
-\begin_layout LyX-Code
- than te end location of the match.
-\end_layout
-
-\begin_layout LyX-Code
-Defining Pairing Rules and Allowing Mismatches, Insertions, and Deletions
-\end_layout
-
-\begin_layout LyX-Code
- Let us stop now and ask "What additional features would one need to
-\end_layout
-
-\begin_layout LyX-Code
- really find the kinds of loop structures that characterize tRNAs,
-\end_layout
-
-\begin_layout LyX-Code
- rRNAs, and so forth?" I can immediately think of two:
-\end_layout
-
-\begin_layout LyX-Code
- a) you will need to be able to allow non-standard pairings
-\end_layout
-
-\begin_layout LyX-Code
- (those other than G-C and A-U), and
-\end_layout
-
-\begin_layout LyX-Code
- b) you will need to be able to tolerate some number of
-\end_layout
-
-\begin_layout LyX-Code
- mismatches and bulges.
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- Let me first show you how to handle non-standard "rules for
-\end_layout
-
-\begin_layout LyX-Code
- pairing in reverse complements".
- Consider the following pattern,
-\end_layout
-
-\begin_layout LyX-Code
- which I show as two line (you may use as many lines as you like in
-\end_layout
-
-\begin_layout LyX-Code
- forming a pattern, although you can only break a pattern at points
-\end_layout
-
-\begin_layout LyX-Code
- where space would be legal):
-\end_layout
-
-\begin_layout LyX-Code
- r1={au,ua,gc,cg,gu,ug,ga,ag}
-\end_layout
-
-\begin_layout LyX-Code
- p1=2...3 0...4 p2=2...5 1...5 r1~p2 0...4 ~p1
-\end_layout
-
-\begin_layout LyX-Code
- The first "pattern unit" does not actually match anything; rather,
-\end_layout
-
-\begin_layout LyX-Code
- it defines a "pairing rule" in which standard pairings are
-\end_layout
-
-\begin_layout LyX-Code
- allowed, as well as G-A and A-G (in case you wondered, Us and Ts
-\end_layout
-
-\begin_layout LyX-Code
- and upper and lower case can be used interchangably; for example
-\end_layout
-
-\begin_layout LyX-Code
- r1={AT,UA,gc,cg} could be used to define the "standard rule" for
-\end_layout
-
-\begin_layout LyX-Code
- pairings).
- The second line consists of six pattern units which
-\end_layout
-
-\begin_layout LyX-Code
- may be interpreted as follows:
-\end_layout
-
-\begin_layout LyX-Code
- p1=2...3 match 2 or 3 characters (call it p1)
-\end_layout
-
-\begin_layout LyX-Code
- 0...4 match 0 to 4 characters
-\end_layout
-
-\begin_layout LyX-Code
- p2=2...5 match 2 to 5 characters (call it p2)
-\end_layout
-
-\begin_layout LyX-Code
- 1...5 match 1 to 5 characters
-\end_layout
-
-\begin_layout LyX-Code
- r1~p2 match the reverse complement of p2,
-\end_layout
-
-\begin_layout LyX-Code
- allowing G-A and A-G pairs
-\end_layout
-
-\begin_layout LyX-Code
- 0...4 match 0 to 4 characters
-\end_layout
-
-\begin_layout LyX-Code
- ~p1 match the reverse complement of p1
-\end_layout
-
-\begin_layout LyX-Code
- allowing only G-C, C-G, A-T, and T-A pairs
-\end_layout
-
-\begin_layout LyX-Code
- Thus, r1~p2 means "match the reverse complement of p2 using rule r1".
-\end_layout
-
-\begin_layout LyX-Code
- Now let us consider the issue of tolerating mismatches and bulges.
-\end_layout
-
-\begin_layout LyX-Code
- You may add a "qualifier" to the pattern unit that gives the
-\end_layout
-
-\begin_layout LyX-Code
- tolerable number of "mismatches, deletions, and insertions".
-\end_layout
-
-\begin_layout LyX-Code
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- p1=10...10 3...8 ~p1[1,2,1]
-\end_layout
-
-\begin_layout LyX-Code
- means that the third pattern unit must match 10 characters,
-\end_layout
-
-\begin_layout LyX-Code
- allowing one "mismatch" (a pairing other than G-C, C-G, A-T, or
-\end_layout
-
-\begin_layout LyX-Code
- T-A), two deletions (a deletion is a character that occurs in p1,
-\end_layout
-
-\begin_layout LyX-Code
- but has been "deleted" from the string matched by ~p1), and one
-\end_layout
-
-\begin_layout LyX-Code
- insertion (an "insertion" is a character that occurs in the string
-\end_layout
-
-\begin_layout LyX-Code
- matched by ~p1, but not for which no corresponding character
-\end_layout
-
-\begin_layout LyX-Code
- occurs in p1).
- In this case, the pattern would match
-\end_layout
-
-\begin_layout LyX-Code
- ACGTACGTAC GGGGGGGG GCGTTACCT
-\end_layout
-
-\begin_layout LyX-Code
- which is, you must admit, a fairly weak loop.
- It is common to
-\end_layout
-
-\begin_layout LyX-Code
- allow mismatches, but you will find yourself using insertions and
-\end_layout
-
-\begin_layout LyX-Code
- deletions much more rarely.
- In any event, you should note that
-\end_layout
-
-\begin_layout LyX-Code
- allowing mismatches, insertions, and deletions does force the
-\end_layout
-
-\begin_layout LyX-Code
- program to try many additional possible pairings, so it does slow
-\end_layout
-
-\begin_layout LyX-Code
- things down a bit.
-\end_layout
-
-\begin_layout LyX-Code
-How Patterns Are Matched
-\end_layout
-
-\begin_layout LyX-Code
- Now is as good a time as any to discuss the basic flow of control
-\end_layout
-
-\begin_layout LyX-Code
- when matching patterns.
- Recall that a "pattern" is a sequence of
-\end_layout
-
-\begin_layout LyX-Code
- "pattern units".
- Suppose that the pattern units were
-\end_layout
-
-\begin_layout LyX-Code
- u1 u2 u3 u4 ...
- un
-\end_layout
-
-\begin_layout LyX-Code
- The scan of a sequence S begins by setting the current position
-\end_layout
-
-\begin_layout LyX-Code
- to 1.
- Then, an attempt is made to match u1 starting at the
-\end_layout
-
-\begin_layout LyX-Code
- current position.
- Each attempt to match a pattern unit can
-\end_layout
-
-\begin_layout LyX-Code
- succeed or fail.
- If it succeeds, then an attempt is made to match
-\end_layout
-
-\begin_layout LyX-Code
- the next unit.
- If it fails, then an attempt is made to find an
-\end_layout
-
-\begin_layout LyX-Code
- alternative match for the immediately preceding pattern unit.
- If
-\end_layout
-
-\begin_layout LyX-Code
- this succeeds, then we proceed forward again to the next unit.
- If
-\end_layout
-
-\begin_layout LyX-Code
- it fails we go back to the preceding unit.
- This process is called
-\end_layout
-
-\begin_layout LyX-Code
- "backtracking".
- If there are no previous units, then the current
-\end_layout
-
-\begin_layout LyX-Code
- position is incremented by one, and everything starts again.
- This
-\end_layout
-
-\begin_layout LyX-Code
- proceeds until either the current position goes past the end of
-\end_layout
-
-\begin_layout LyX-Code
- the sequence or all of the pattern units succeed.
- On success,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches reports the "hit", the current position is set
-\end_layout
-
-\begin_layout LyX-Code
- just past the hit, and an attempt is made to find another hit.
-\end_layout
-
-\begin_layout LyX-Code
- If you wish to limit the scan to simply finding a maximum of, say,
-\end_layout
-
-\begin_layout LyX-Code
- 10 hits, you can use the -n option (-n 10 would set the limit to
-\end_layout
-
-\begin_layout LyX-Code
- 10 reported hits).
- For example,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches -c -n 1 pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- would search for just the first hit (and would stop searching the
-\end_layout
-
-\begin_layout LyX-Code
- current sequences or any that follow in the input file).
-\end_layout
-
-\begin_layout LyX-Code
-Searching for repeats:
-\end_layout
-
-\begin_layout LyX-Code
- In the last section, I discussed almost all of the details
-\end_layout
-
-\begin_layout LyX-Code
- required to allow you to look for repeats.
- Consider the following
-\end_layout
-
-\begin_layout LyX-Code
- set of patterns:
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...6 3...8 p1 (find exact 6 character repeat separated
-\end_layout
-
-\begin_layout LyX-Code
- by to 8 characters)
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...6 3..8 p1[1,0,0] (allow one mismatch)
-\end_layout
-
-\begin_layout LyX-Code
- p1=3...3 p1[1,0,0] p1[1,0,0] p1[1,0,0]
-\end_layout
-
-\begin_layout LyX-Code
- (match 12 characters that are the remains
-\end_layout
-
-\begin_layout LyX-Code
- of a 3-character sequence occurring 4 times)
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...8 0...3 p2=6...8 p1 0...3 p2
-\end_layout
-
-\begin_layout LyX-Code
- (This would match things like
-\end_layout
-
-\begin_layout LyX-Code
- ATCT G TCTTT ATCT TG TCTTT
-\end_layout
-
-\begin_layout LyX-Code
- )
-\end_layout
-
-\begin_layout LyX-Code
-Searching for particular sequences:
-\end_layout
-
-\begin_layout LyX-Code
- Occasionally, one wishes to match a specific, known sequence.
-\end_layout
-
-\begin_layout LyX-Code
- In such a case, you can just give the sequence (along with an
-\end_layout
-
-\begin_layout LyX-Code
- optional statement of the allowable mismatches, insertions, and
-\end_layout
-
-\begin_layout LyX-Code
- deletions).
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...8 GAGA ~p1 (match a hairpin with GAGA as the loop)
-\end_layout
-
-\begin_layout LyX-Code
- RRRRYYYY (match 4 purines followed by 4 pyrimidines)
-\end_layout
-
-\begin_layout LyX-Code
- TATAA[1,0,0] (match TATAA, allowing 1 mismatch)
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-Matches against a "weight matrix":
-\end_layout
-
-\begin_layout LyX-Code
- I will conclude my examples of the types of pattern units
-\end_layout
-
-\begin_layout LyX-Code
- available for matching against nucleotide sequences by discussing a
-\end_layout
-
-\begin_layout LyX-Code
- crude implemetation of matching using a "weight matrix".
- While I
-\end_layout
-
-\begin_layout LyX-Code
- am less than overwhelmed with the syntax that I chose, I think that
-\end_layout
-
-\begin_layout LyX-Code
- the reader should be aware that I was thinking of generating
-\end_layout
-
-\begin_layout LyX-Code
- patterns containing such pattern units automatically from
-\end_layout
-
-\begin_layout LyX-Code
- alignments (and did not really plan on typing such things in by
-\end_layout
-
-\begin_layout LyX-Code
- hand very often).
- Anyway, suppose that you wanted to match a
-\end_layout
-
-\begin_layout LyX-Code
- sequence of eight characters.
- The "consensus" of these eight
-\end_layout
-
-\begin_layout LyX-Code
- characters is GRCACCGS, but the actual "frequencies of occurrence"
-\end_layout
-
-\begin_layout LyX-Code
- are given in the matrix below.
- Thus, the first character is an A
-\end_layout
-
-\begin_layout LyX-Code
- 16% the time and a G 84% of the time.
- The second is an A 57% of
-\end_layout
-
-\begin_layout LyX-Code
- the time, a C 10% of the time, a G 29% of the time, and a T 4% of
-\end_layout
-
-\begin_layout LyX-Code
- the time.
-
-\end_layout
-
-\begin_layout LyX-Code
- C1 C2 C3 C4 C5 C6 C7 C8
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- A 16 57 0 95 0 18 0 0
-\end_layout
-
-\begin_layout LyX-Code
- C 0 10 80 0 100 60 0 50
-\end_layout
-
-\begin_layout LyX-Code
- G 84 29 0 0 0 20 100 50
-\end_layout
-
-\begin_layout LyX-Code
- T 0 4 20 5 0 2 0 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- One could use the following pattern unit to search for inexact
-\end_layout
-
-\begin_layout LyX-Code
- matches related to such a "weight matrix":
-\end_layout
-
-\begin_layout LyX-Code
- {(16,0,84,0),(57,10,29,4),(0,80,0,20),(95,0,0,5),
-\end_layout
-
-\begin_layout LyX-Code
- (0,100,0,0),(18,60,20,2),(0,0,100,0),(0,50,50,0)} > 450
-\end_layout
-
-\begin_layout LyX-Code
- This pattern unit will attempt to match exactly eight characters.
-\end_layout
-
-\begin_layout LyX-Code
- For each character in the sequence, the entry in the corresponding
-\end_layout
-
-\begin_layout LyX-Code
- tuple is added to an accumulated sum.
- If the sum is greater than
-\end_layout
-
-\begin_layout LyX-Code
- 450, the match succeeds; else it fails.
-\end_layout
-
-\begin_layout LyX-Code
- Recently, this feature was upgraded to allow ranges.
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- 600 > {(16,0,84,0),(57,10,29,4),(0,80,0,20),(95,0,0,5),
-\end_layout
-
-\begin_layout LyX-Code
- (0,100,0,0),(18,60,20,2),(0,0,100,0),(0,50,50,0)} > 450
-\end_layout
-
-\begin_layout LyX-Code
- will work, as well.
-\end_layout
-
-\begin_layout LyX-Code
-Allowing Alternatives:
-\end_layout
-
-\begin_layout LyX-Code
- Very occasionally, you may wish to allow alternative pattern units
-\end_layout
-
-\begin_layout LyX-Code
- (i.e., "match either A or B").
- You can do this using something
-\end_layout
-
-\begin_layout LyX-Code
- like
-\end_layout
-
-\begin_layout LyX-Code
- ( GAGA | GCGCA)
-\end_layout
-
-\begin_layout LyX-Code
- which says "match either GAGA or GCGCA".
- You may take
-\end_layout
-
-\begin_layout LyX-Code
- alternatives of a list of pattern units, for example
-\end_layout
-
-\begin_layout LyX-Code
- (p1=3...3 3...8 ~p1 | p1=5...5 4...4 ~p1 GGG)
-\end_layout
-
-\begin_layout LyX-Code
- would match one of two sequences of pattern units.
- There is one
-\end_layout
-
-\begin_layout LyX-Code
- clumsy aspect of the syntax: to match a list of alternatives, you
-\end_layout
-
-\begin_layout LyX-Code
- need to fully the request.
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- (GAGA | (GCGCA | TTCGA))
-\end_layout
-
-\begin_layout LyX-Code
- would be needed to try the three alternatives.
-\end_layout
-
-\begin_layout LyX-Code
-One Minor Extension
-\end_layout
-
-\begin_layout LyX-Code
- Sometimes a pattern will contain a sequence of distinct ranges,
-\end_layout
-
-\begin_layout LyX-Code
- and you might wish to limit the sum of the lengths of the matched
-\end_layout
-
-\begin_layout LyX-Code
- subsequences.
- For example, suppose that you basically wanted to
-\end_layout
-
-\begin_layout LyX-Code
- match something like
-\end_layout
-
-\begin_layout LyX-Code
- ARRYYTT p1=0...5 GCA[1,0,0] p2=1...6 ~p1 4...8 ~p2 p3=4...10 CCT
-\end_layout
-
-\begin_layout LyX-Code
- but that the sum of the lengths of p1, p2, and p3 must not exceed
-\end_layout
-
-\begin_layout LyX-Code
- eight characters.
- To do this, you could add
-\end_layout
-
-\begin_layout LyX-Code
- length(p1+p2+p3) < 9
-\end_layout
-
-\begin_layout LyX-Code
- as the last pattern unit.
- It will just succeed or fail (but does
-\end_layout
-
-\begin_layout LyX-Code
- not actually match any characters in the sequence).
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-Matching Protein Sequences
-\end_layout
-
-\begin_layout LyX-Code
- Suppose that the input file contains protein sequences.
- In this
-\end_layout
-
-\begin_layout LyX-Code
- case, you must invoke scan_for_matches with the "-p" option.
- You
-\end_layout
-
-\begin_layout LyX-Code
- cannot use aspects of the language that relate directly to
-\end_layout
-
-\begin_layout LyX-Code
- nucleotide sequences (e.g., the -c command line option or pattern
-\end_layout
-
-\begin_layout LyX-Code
- constructs referring to the reverse complement of a previously
-\end_layout
-
-\begin_layout LyX-Code
- matched unit).
-
-\end_layout
-
-\begin_layout LyX-Code
- You also have two additional constructs that allow you to match
-\end_layout
-
-\begin_layout LyX-Code
- either "one of a set of amino acids" or "any amino acid other than
-\end_layout
-
-\begin_layout LyX-Code
- those a given set".
- For example,
-\end_layout
-
-\begin_layout LyX-Code
- p1=0...4 any(HQD) 1...3 notany(HK) p1
-\end_layout
-
-\begin_layout LyX-Code
- would successfully match a string like
-\end_layout
-
-\begin_layout LyX-Code
- YWV D AA C YWV
-\end_layout
-
-\begin_layout LyX-Code
-Using the show_hits Utility
-\end_layout
-
-\begin_layout LyX-Code
- When viewing a large set of complex matches, you might find it
-\end_layout
-
-\begin_layout LyX-Code
- convenient to post-process the scan_for_matches output to get a
-\end_layout
-
-\begin_layout LyX-Code
- more readable version.
- We provide a simple post-processor called
-\end_layout
-
-\begin_layout LyX-Code
- "show_hits".
- To see its effect, just pipe the output of a
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches into show_hits:
-\end_layout
-
-\begin_layout LyX-Code
- Normal Output:
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches -c pat_file < tmp
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[1,28]
-\end_layout
-
-\begin_layout LyX-Code
- gtacguaacc ggttaac cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[28,1]
-\end_layout
-
-\begin_layout LyX-Code
- gtacgtaacc ggttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- >tst2:[2,31]
-\end_layout
-
-\begin_layout LyX-Code
- CGTACGUAAC C GGTTAACC GGUUACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- >tst2:[31,2]
-\end_layout
-
-\begin_layout LyX-Code
- CGTACGTAAC C GGTTAACC GGTTACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- >tst3:[3,32]
-\end_layout
-
-\begin_layout LyX-Code
- gtacguaacc g gttaactt cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- >tst3:[32,3]
-\end_layout
-
-\begin_layout LyX-Code
- gtacgtaacc g aagttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- Piped Through show_hits:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches -c pat_file < tmp | show_hits
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[1,28]: gtacguaacc ggttaac cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[28,1]: gtacgtaacc ggttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[2,31]: CGTACGUAAC C GGTTAACC GGUUACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[31,2]: CGTACGTAAC C GGTTAACC GGTTACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[3,32]: gtacguaacc g gttaactt cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[32,3]: gtacgtaacc g aagttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- clone%
-\end_layout
-
-\begin_layout LyX-Code
- Optionally, you can specify which of the "fields" in the matches
-\end_layout
-
-\begin_layout LyX-Code
- you wish to sort on, and show_hits will sort them.
- The field
-\end_layout
-
-\begin_layout LyX-Code
- numbers start with 0.
- So, you might get something like
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches -c pat_file < tmp | show_hits 2 1
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[2,31]: CGTACGUAAC C GGTTAACC GGUUACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[31,2]: CGTACGTAAC C GGTTAACC GGTTACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[32,3]: gtacgtaacc g aagttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[1,28]: gtacguaacc ggttaac cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[28,1]: gtacgtaacc ggttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[3,32]: gtacguaacc g gttaactt cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- clone%
-\end_layout
-
-\begin_layout LyX-Code
- In this case, the hits have been sorted on fields 2 and 1 (that is,
-\end_layout
-
-\begin_layout LyX-Code
- the third and second matched subfields).
-\end_layout
-
-\begin_layout LyX-Code
- show_hits is just one possible little post-processor, and you
-\end_layout
-
-\begin_layout LyX-Code
- might well wish to write a customized one for yourself.
-\end_layout
-
-\begin_layout LyX-Code
-Reducing the Cost of a Search
-\end_layout
-
-\begin_layout LyX-Code
- The scan_for_matches utility uses a fairly simple search, and may
-\end_layout
-
-\begin_layout LyX-Code
- consume large amounts of CPU time for complex patterns.
- Someday,
-\end_layout
-
-\begin_layout LyX-Code
- I may decide to optimize the code.
- However, until then, let me
-\end_layout
-
-\begin_layout LyX-Code
- mention one useful technique.
-
-\end_layout
-
-\begin_layout LyX-Code
- When you have a complex pattern that includes a number of varying
-\end_layout
-
-\begin_layout LyX-Code
- ranges, imprecise matches, and so forth, it is useful to
-\end_layout
-
-\begin_layout LyX-Code
- "pipeline" matches.
- That is, form a simpler pattern that can be
-\end_layout
-
-\begin_layout LyX-Code
- used to scan through a large database extracting sections that
-\end_layout
-
-\begin_layout LyX-Code
- might be matched by the more complex pattern.
- Let me illustrate
-\end_layout
-
-\begin_layout LyX-Code
- with a short example.
- Suppose that you really wished to match the
-\end_layout
-
-\begin_layout LyX-Code
- pattern
-\end_layout
-
-\begin_layout LyX-Code
- p1=3...5 0...8 ~p1[1,1,0] p2=6...7 3...6 AGC 3...5 RYGC ~p2[1,0,0]
-\end_layout
-
-\begin_layout LyX-Code
- In this case, the pattern units AGC 3...5 RYGC can be used to rapidly
-\end_layout
-
-\begin_layout LyX-Code
- constrain the overall search.
- You can preprocess the overall
-\end_layout
-
-\begin_layout LyX-Code
- database using the pattern:
-\end_layout
-
-\begin_layout LyX-Code
- 31...31 AGC 3...5 RYGC 7...7
-\end_layout
-
-\begin_layout LyX-Code
- Put the complex pattern in pat_file1 and the simpler pattern in
-\end_layout
-
-\begin_layout LyX-Code
- pat_file2.
- Then use,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches -c pat_file2 < nucleotide_database |
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches pat_file1
-\end_layout
-
-\begin_layout LyX-Code
- The output will show things like
-\end_layout
-
-\begin_layout LyX-Code
- >seqid:[232,280][2,47]
-\end_layout
-
-\begin_layout LyX-Code
- matches pieces
-\end_layout
-
-\begin_layout LyX-Code
- Then, the actual section of the sequence that was matched can be
-\end_layout
-
-\begin_layout LyX-Code
- easily computed as [233,278] (remember, the positions start from
-\end_layout
-
-\begin_layout LyX-Code
- 1, not 0).
-\end_layout
-
-\begin_layout LyX-Code
- Let me finally add, you should do a few short experiments to see
-\end_layout
-
-\begin_layout LyX-Code
- whether or not such pipelining actually improves performance -- it
-\end_layout
-
-\begin_layout LyX-Code
- is not always obvious where the time is going, and I have
-\end_layout
-
-\begin_layout LyX-Code
- sometimes found that the added complexity of pipelining actually
-\end_layout
-
-\begin_layout LyX-Code
- slowed things up.
- It gets its best improvements when there are
-\end_layout
-
-\begin_layout LyX-Code
- exact matches of more than just a few characters that can be
-\end_layout
-
-\begin_layout LyX-Code
- rapidly used to eliminate large sections of the database.
-\end_layout
-
-\begin_layout LyX-Code
-=============
-\end_layout
-
-\begin_layout LyX-Code
-Additions:
-\end_layout
-
-\begin_layout LyX-Code
-Feb 9, 1995: the pattern units ^ and $ now work as in normal regular
-\end_layout
-
-\begin_layout LyX-Code
- expressions.
- That is
-\end_layout
-
-\begin_layout LyX-Code
- TTF $
-\end_layout
-
-\begin_layout LyX-Code
- matches only TTF at the end of the string and
-\end_layout
-
-\begin_layout LyX-Code
- ^ TTF
-\end_layout
-
-\begin_layout LyX-Code
- matches only an initial TTF
-\end_layout
-
-\begin_layout LyX-Code
- The pattern unit
-\end_layout
-
-\begin_layout LyX-Code
- <p1
-\end_layout
-
-\begin_layout LyX-Code
- matches the reverse of the string named p1.
- That is,
-\end_layout
-
-\begin_layout LyX-Code
- if p1 matched GCAT, then <p1 would match TACG.
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...6 <p1
-\end_layout
-
-\begin_layout LyX-Code
- matches a real palindrome (not the biologically common
-\end_layout
-
-\begin_layout LyX-Code
- meaning of "reverse complement")
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\end_body
-\end_document
+++ /dev/null
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
-\begin_document
-\begin_header
-\textclass scrartcl
-\begin_preamble
-\usepackage[colorlinks=true, urlcolor=blue, linkcolor=black]{hyperref}
-\end_preamble
-\language english
-\inputencoding auto
-\font_roman default
-\font_sans default
-\font_typewriter default
-\font_default_family default
-\font_sc false
-\font_osf false
-\font_sf_scale 100
-\font_tt_scale 100
-\graphics default
-\paperfontsize default
-\spacing single
-\papersize default
-\use_geometry false
-\use_amsmath 1
-\use_esint 1
-\cite_engine basic
-\use_bibtopic false
-\paperorientation portrait
-\secnumdepth 3
-\tocdepth 3
-\paragraph_separation skip
-\defskip medskip
-\quotes_language english
-\papercolumns 1
-\papersides 1
-\paperpagestyle default
-\tracking_changes false
-\output_changes false
-\author ""
-\author ""
-\end_header
-
-\begin_body
-
-\begin_layout Title
-Biotools Cookbook
-\end_layout
-
-\begin_layout Author
-Martin Asser Hansen
-\end_layout
-
-\begin_layout Publishers
-John Mattick Group
-\newline
-Institute for Molecular Bioscience
-\newline
-University of Queensland
-\newline
-Aust
-ralia
-\newline
-E-mail: mail@maasha.dk
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
-
-\backslash
-thispagestyle{empty}
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-
-\newpage
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset LatexCommand tableofcontents
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset FloatList figure
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-
-\newpage
-
-\end_layout
-
-\begin_layout Section
-Introduction
-\end_layout
-
-\begin_layout Standard
-Biotools is a selection of simple tools that can be linked together (piped
- as we shall call it) in a very flexible manner to perform both simple and
- complex tasks.
- The fundamental idea is that biotools work on a data stream that will only
- terminate at the end of an analysis and that this data stream can be passed
- through several different biotools, each performing one specific task.
- The advantage of this approach is that a user can perform simple and complex
- tasks without having to write advanced code.
- Moreover, since the data format used to pass data between biotools is text
- based, biotools can be written by different developers in their favorite
- programming language --- and still the biotools will be able to work together.
-\end_layout
-
-\begin_layout Standard
-In the most simple form bioools can be piped together on the command line
- like this (using the pipe character '|'):
-\end_layout
-
-\begin_layout LyX-Code
-read_data | calculate_something | write_result
-\end_layout
-
-\begin_layout Standard
-However, a more comprehensive analysis could be composed:
-\end_layout
-
-\begin_layout LyX-Code
-read_data | select_entries | convert_entries | search_database
-\end_layout
-
-\begin_layout LyX-Code
-evaluate_results | plot_diagram | plot_another_diagram |
-\end_layout
-
-\begin_layout LyX-Code
-load_to_database
-\end_layout
-
-\begin_layout Standard
-The data stream that is piped through the biotools consists of records of
- key/value pairs in the same way a hash does in order to keep as simple
- a structure as possible.
- An example record can be seen below:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-REC_TYPE: PATSCAN
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-MATCH: AGATCAAGTG
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-S_BEG: 7
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-S_END: 16
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-ALIGN_LEN: 9
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-S_ID: piR-t6
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-STRAND: +
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-PATTERN: AGATCAAGTG
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
----
-\end_layout
-
-\begin_layout Standard
-The '
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-' denotes the delimiter of the records, and each key is a word followed
- by a ':' and a white-space and then the value.
- By convention the biotools only uses upper case keys (a list of used keys
- can be seen in Appendix\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sec:Keys"
-
-\end_inset
-
-).
- Since the records basically are hash structures this mean that the order
- of the keys in the stream is unordered, and in the above example it is
- pure coincidence that HIT_BEG is displayed before HIT_END, however, when
- the order of the keys is importent, the biotools will automagically see
- to that.
-\end_layout
-
-\begin_layout Standard
-All of the biotools are able to read and write a data stream to and from
- file as long as the records are in the biotools format.
- This means that if you are undertaking a lengthy analysis where one of
- the steps is time consuming, you may save the stream after this step, and
- subsequently start one or more analysis from that last step
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-It is a goal that the biotools at some point will be able to dump the data
- stream to file in case one of the tools fail critically.
-\end_layout
-
-\end_inset
-
-.
- If you are running a lengthy analysis it is highly recommended that you
- create a small test sample of the data and run that through the pipeline
- --- and once you are satisfied with the result proceed with the full data
- set (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-select-a-few-records"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Standard
-All of the biotools can be supplied with long arguments prefixed with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
- switches or single character arguments prefixed with - switches that can
- be grouped together (e.g.
- -xok).
- In this cookbook only the long switches are used to emphasize what these
- switches do.
-\end_layout
-
-\begin_layout Section
-Setup
-\end_layout
-
-\begin_layout Standard
-In order to get the biotools to work, you need to add environment settings
- to include the code binaries, scripts, and modules that constitute the
- biotools package.
- Assuming that you are using bash, add the following to your '~/.bashrc'
- file using your favorite editor.
- After the changes has been saved you need to either run 'source ~/.bashrc'
- or relogin.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-# >>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-# Stuff that enables biotools.
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-export TOOLS_DIR="/home/m.hansen/tools" # Contains binaries for BLAST
- and Vmatch.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-export INST_DIR="/home/m.hansen/maasha" # Contains scripts and modules.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-export DATA_DIR="/home/m.hansen/DATA" # Contains genomic data etc.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-export TMP_DIR="/home/m.hansen/maasha/tmp" # Required temporary directory.
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-export PATH="$PATH:$TOOLS_DIR/blast-2.2.17/bin:$TOOLS_DIR/vmatch.distribution"
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-export PATH="$INST_DIR/bin/:$INST_DIR/perl_scripts/:$INST_DIR/perl_scripts/b
-iotools:$PATH"
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-export PERL5LIB="$PERL5LIB:$INST_DIR"
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-# Alias allowing power scripting with biotools
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-alias bioscript="perl -I $INST_DIR/Maasha -MBiotools=read_stream,get_recor
-d,put_record -e"
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-# >>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<
-\end_layout
-
-\begin_layout Section
-Getting Started
-\end_layout
-
-\begin_layout Standard
-The biotool
-\series bold
-list_biotools
-\series default
- lists all the biotools along with a description:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-list_biotools
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-align_seq Align sequences in stream using Muscle.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-analyze_seq Analysis the residue composition of each sequence
- in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-analyze_vals Determine type, count, min, max, sum and mean for
- values in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-blast_seq BLAST sequences in stream against a specified database.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-blat_seq BLAT sequences in stream against a specified genome.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-complement_seq Complement sequences in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_records Count the number of records in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_seq Count sequences in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_vals Count the number of times values of given keys exists
- in stream.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-create_blast_db Create a BLAST database from sequences in stream for
- use with BLAST.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-...
-\end_layout
-
-\begin_layout Standard
-To list the biotools for writing different formats, you can use unix's grep
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-list_biotools | grep write
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_align Write aligned sequences in pretty alignment format.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_bed Write records from stream as BED lines.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_blast Write BLAST records from stream in BLAST tabular format
- (-m8 and 9).
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_fasta Write sequences in FASTA format.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_psl Write records from stream in PSL format.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-write_tab Write records from stream as tab separated table.
-\end_layout
-
-\begin_layout Standard
-In order to find out how a specific biotool works, you just type the program
- name without any arguments and press return and the usage of the biotool
- will be displayed.
- E.g.
-
-\series bold
-read_fasta
-\series default
- <return>:
-\end_layout
-
-\begin_layout Standard
-\begin_inset Box Frameless
-position "t"
-hor_pos "c"
-has_inner_box 1
-inner_pos "t"
-use_parbox 0
-width "100col%"
-special "none"
-height "1in"
-height_special "totalheight"
-status open
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Program name: read_fasta
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Contact: mail@maasha.dk
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Date: August 2007
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/
-gpl.html)
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Description: Read FASTA entries.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Usage: read_fasta [options] -i <FASTA file(s)>
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Options:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-i <file(s)> | --data_in=<file(s)>] - Comma separated list of files
- to read.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-n <int> | --num=<int>] - Limit number of records to read.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-I <file> | --stream_in=<file>] - Read input stream from file
- - Default=STDIN
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- [-O <file> | --stream_out=<file>] - Write output stream to file
- - Default=STDOUT
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-Examples:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i test.fna - Read FASTA entries from file.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i test1.fna,test2,fna - Read FASTA entries from files.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i '*.fna' - Read FASTA entries from files.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
- read_fasta -i test.fna -n 10 - Read first 10 FASTA entries from
- file.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Section
-The Data Stream
-\end_layout
-
-\begin_layout Subsection
-How to read the data stream from file?
-\begin_inset LatexCommand label
-name "sub:How-to-read-stream"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-You want to read a data stream that you previously have saved to file in
- biotools format.
- This can be done implicetly or explicitly.
- The implicit way uses the 'stdout' stream of the Unix terminal:
-\end_layout
-
-\begin_layout LyX-Code
-cat | <biotool>
-\end_layout
-
-\begin_layout Standard
-cat is the Unix command that reads a file and output the result to 'stdout'
- --- which in this case is piped to any biotool represented by the <biotool>.
- It is also possible to read the data stream using '<' to direct the 'stdout'
- stream into the biotool like this:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> < <file>
-\end_layout
-
-\begin_layout Standard
-However, that will not work if you pipe more biotools together.
- Then it is much safer to read the stream from a file explicitly like this:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --stream_in=<file>
-\end_layout
-
-\begin_layout Standard
-Here the filename <file> is explicetly given to the biotool <biotool> with
- the switch
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_in.
- This switch works with all biotools.
- It is also possible to read in data from multiple sources by repeating
- the explicit read step:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --stream_in=<file1> | <biotool> --stream_in=<file2>
-\end_layout
-
-\begin_layout Subsection
-How to write the data stream to file?
-\begin_inset LatexCommand label
-name "sub:How-to-write-stream"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-In order to save the output stream from a biotool to file, so you can read
- in the stream again at a later time, you can do one of two things:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> > <file>
-\end_layout
-
-\begin_layout Standard
-All, the biotools write the data stream to 'stdout' by default which can
- be written to a file by redirecting 'stdout' to file using '>' , however,
- if one of the biotools for writing other formats is used then the both
- the biotools records as well as the result output will go to 'stdout' in
- a mixture causing havock! To avoid this you must use the switch
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_out that explictly tells the biotool to write the output stream to
- file:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --stream_out=<file>
-\end_layout
-
-\begin_layout Standard
-The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_out switch works with all biotools.
-\end_layout
-
-\begin_layout Subsection
-How to terminate the data stream?
-\end_layout
-
-\begin_layout Standard
-The data stream is never stops unless the user want to save the stream or
- by supplying the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch that will terminate the stream:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --no_stream
-\end_layout
-
-\begin_layout Standard
-The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch only works with those biotools where it makes sense that
- the user might want to terminale the data stream,
-\emph on
-i.e
-\emph default
-.
- after an analysis step where the user wants to output the result, but not
- the data stream.
-\end_layout
-
-\begin_layout Subsection
-How to write my results to file?
-\begin_inset LatexCommand label
-name "sub:How-to-write-result"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Saving the result of an analysis to file can be done implicitly or explicitly.
- The implicit way:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --no_stream > <file>
-\end_layout
-
-\begin_layout Standard
-If you use '>' to redirect 'stdout' to file then it is important to use
- the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch to avoid writing a mix of biotools records and result to
- the same file causing havock.
- The safe way is to use the
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out switch which explicetly tells the biotool to write the result
- to a given file:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --result_out=<file>
-\end_layout
-
-\begin_layout Standard
-Using the above method will not terminate the stream, so it is possible
- to pipe that into another biotool generating different results:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool1> --result_out=<file1> | <biotool2> --result_out=<file2>
-\end_layout
-
-\begin_layout Standard
-And still the data stream will continue unless terminated with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --result_out=<file> --no_stream
-\end_layout
-
-\begin_layout Standard
-Or written to file using implicitly or explicity
-\begin_inset LatexCommand eqref
-reference "sub:How-to-write-result"
-
-\end_inset
-
-.
- The explicit way:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --result_out=<file1> --stream_out=<file2>
-\end_layout
-
-\begin_layout Subsection
-How to read data from multiple sources?
-\end_layout
-
-\begin_layout Standard
-To read multiple data sources, with the same type or different type of data
- do:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool1> --data_in=<file1> | <biotool2> --data_in=<file2>
-\end_layout
-
-\begin_layout Standard
-where type is the data type a specific biotool reads.
-\end_layout
-
-\begin_layout Section
-Reading input
-\end_layout
-
-\begin_layout Subsection
-How to read biotools input?
-\end_layout
-
-\begin_layout Standard
-See
-\begin_inset LatexCommand eqref
-reference "sub:How-to-read-stream"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Subsection
-How to read in data?
-\end_layout
-
-\begin_layout Standard
-Data in different formats can be read with the appropriate biotool for that
- format.
- The biotools are typicalled named 'read_<data type>' such as
-\series bold
-read_fasta
-\series default
-,
-\series bold
-read_bed
-\series default
-,
-\series bold
-read_tab
-\series default
-, etc., and all behave in a similar manner.
- Data can be read by supplying the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-data_in switch and a file name to the file containing the data:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --data_in=<file>
-\end_layout
-
-\begin_layout Standard
-It is also possible to read in a saved biotools stream (see
-\begin_inset LatexCommand ref
-reference "sub:How-to-read-stream"
-
-\end_inset
-
-) as well as reading data in one go:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --stream_in=<file1> --data_in=<file2>
-\end_layout
-
-\begin_layout Standard
-If you want to read data from several files you can do this:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --data_in=<file1> | <biotool> --data_in=<file2>
-\end_layout
-
-\begin_layout Standard
-If you have several data files you can read in all explicitly with a comma
- separated list:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --data_in=file1,file2,file3
-\end_layout
-
-\begin_layout Standard
-And it is also possible to use file globbing
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-using the short option will only work if you quote the argument -i '*.fna'
-\end_layout
-
-\end_inset
-
-:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --data_in=*.fna
-\end_layout
-
-\begin_layout Standard
-Or in a combination:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool> --data_in=file1,/dir/*.fna
-\end_layout
-
-\begin_layout Standard
-Finally, it is possible to read in data in different formats using the appropria
-te biotool for each format:
-\end_layout
-
-\begin_layout LyX-Code
-<biotool1> --data_in=<file1> | <biotool2> --data_in=<file2> ...
-\end_layout
-
-\begin_layout Subsection
-How to read FASTA input?
-\end_layout
-
-\begin_layout Standard
-Sequences in FASTA format can be read explicitly using
-\series bold
-read_fasta
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file>
-\end_layout
-
-\begin_layout Subsection
-How to read alignment input?
-\end_layout
-
-\begin_layout Standard
-If your alignment if FASTA formatted then you can
-\series bold
-read_align
-\series default
-.
- It is also possible to use
-\series bold
-read_fasta
-\series default
- since the data is FASTA formatted, however, with
-\series bold
-read_fasta
-\series default
- the key ALIGN will be omitted.
- The ALIGN key is used to determine which sequences belong to what alignment
- which is required for
-\series bold
-write_align
-\series default
-.
-\end_layout
-
-\begin_layout LyX-Code
-read_align --data_in=<file>
-\end_layout
-
-\begin_layout Subsection
-How to read tabular input?
-\begin_inset LatexCommand label
-name "sub:How-to-read-table"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Tabular input can be read with
-\series bold
-read_tab
-\series default
- which will read in all rows and chosen columns (separated by a given delimter)
- from a table in text format.
-\end_layout
-
-\begin_layout Standard
-The table below:
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Tabular
-<lyxtabular version="3" rows="4" columns="3">
-<features>
-<column alignment="left" valignment="top" width="0">
-<column alignment="left" valignment="top" width="0">
-<column alignment="left" valignment="top" width="0">
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Human
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-ATACGTCAG
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-23524
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Dog
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-AGCATGAC
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-2442
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Mouse
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-GACTG
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-234
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Cat
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-AAATGCA
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-2342
-\end_layout
-
-\end_inset
-</cell>
-</row>
-</lyxtabular>
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Can be read using the command:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file>
-\end_layout
-
-\begin_layout Standard
-Which will result in four records, one for each row, where the keys V0,
- V1, V2 are the default keys for the organism, sequence, and count, respectively.
- It is possible to select a subset of colums to read by using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-cols switch which takes a comma separated list of columns numbers (first
- column is designated 0) as argument.
- So to read in only the sequence and the count so that the count comes before
- the sequence do:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file> --cols=2,1
-\end_layout
-
-\begin_layout Standard
-It is also possible to name the columns with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys switch:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file> --cols=2,1 --keys=COUNT,SEQ
-\end_layout
-
-\begin_layout Subsection
-How to read BED input?
-\end_layout
-
-\begin_layout Standard
-The BED (Browser Extensible Data
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://genome.ucsc.edu/FAQ/FAQformat"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-) format is a tabular format for data pertaining to one of the Eukaryotic
- genomes in the UCSC genome brower
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://genome.ucsc.edu/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-.
- The BED format consists of up to 12 columns, where the first three are
- mandatory CHR, CHR_BEG, and CHR_END.
- The mandatory columns and any of the optional columns can all be read in
- easily with the
-\series bold
-read_bed
-\series default
- biotool.
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<file>
-\end_layout
-
-\begin_layout Standard
-It is also possible to read the BED file with
-\series bold
-read_tab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-read-table"
-
-\end_inset
-
-), however, that will be more cumbersome because you need to specify the
- keys:
-\end_layout
-
-\begin_layout LyX-Code
-read_tab --data_in=<file> --keys=CHR,CHR_BEG,CHR_END ...
-\end_layout
-
-\begin_layout Subsection
-How to read PSL input?
-\end_layout
-
-\begin_layout Standard
-The PSL format is the output from BLAT and contains 21 mandatory fields
- that can be read with
-\series bold
-read_psl
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-read_psl --data_in=<file>
-\end_layout
-
-\begin_layout Section
-Writing output
-\end_layout
-
-\begin_layout Standard
-All result output can be written explicitly to file using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out switch which all result generating biotools have.
- It is also possible to write the result to file implicetly by directing
- 'stdout' to file using '>', however, that requires the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream swich to prevent a mixture of data stream and results in the file.
- The explicit (and safe) way:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | <biotool> --result_out=<file>
-\end_layout
-
-\begin_layout Standard
-The implicit way:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | <biotool> --no_stream > <file>
-\end_layout
-
-\begin_layout Subsection
-How to write biotools output?
-\end_layout
-
-\begin_layout Standard
-See
-\begin_inset LatexCommand eqref
-reference "sub:How-to-write-stream"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Subsection
-How to write FASTA output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-fasta"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-FASTA output can be written with
-\series bold
-write_fasta
-\series default
-.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_fasta --result_out=<file>
-\end_layout
-
-\begin_layout Standard
-It is also possible to wrap the sequences to a given width using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-wrap switch allthough wrapping of sequence is generally an evil thing:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_fasta --no_stream --wrap=80
-\end_layout
-
-\begin_layout Subsection
-How to write alignment output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-alignment"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Pretty alignments with ruler
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-'.' for every 10 residues, ':' for every 50, and '|' for every 100
-\end_layout
-
-\end_inset
-
- and consensus sequence
-\begin_inset Note Note
-status collapsed
-
-\begin_layout Standard
-which reminds me to make that an option.
-\end_layout
-
-\end_inset
-
- can be created with
-\series bold
-write_align
-\series default
-, what also have the optional
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-wrap switch to break the alignment into blocks of a given width:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_align --result_out=<file> --wrap=80
-\end_layout
-
-\begin_layout Standard
-If the number of sequnces in the alignment is 2 then a pairwise alignment
- will be output otherwise a multiple alignment.
- And if the sequence type, determined automagically, is protein, then residues
- and symbols (+,\InsetSpace ~
-:,\InsetSpace ~
-.) will be used to show consensus according to the Blosum62
- matrix.
-\end_layout
-
-\begin_layout Subsection
-How to write tabular output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-tab"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Outputting the data stream as a table can be done with
-\series bold
-write_tab
-\series default
-, which will write generate one row per record with the values as columns.
- If you supply the optional
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-comment switch, when the first row in the table will be a 'comment' line
- prefixed with a '#':
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --comment
-\end_layout
-
-\begin_layout Standard
-You can also change the delimiter from the default (tab) to
-\emph on
-e.g.
-
-\emph default
- ',':
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --delimit=','
-\end_layout
-
-\begin_layout Standard
-If you want the values output in a specific order you have to supply a comma
- separated list using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys switch that will print only those keys in that order:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --keys=SEQ_NAME,COUNT
-\end_layout
-
-\begin_layout Standard
-Alternatively, if you have some keys that you don't want in the tabular
- output, use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_keys switch.
- So to print all keys except SEQ and SEQ_TYPE do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | write_tab --result_out=<file> --no_keys=SEQ,SEQ_TYPE
-\end_layout
-
-\begin_layout Standard
-Finally, if you have a stream containing a mix of different records types,
-
-\emph on
-e.g.
-
-\emph default
- records with sequences and records with matches, then you can use
-\series bold
-write_tab
-\series default
- to output all the records in tabluar format, however, the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-comment,
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys, and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_keys switches will only respond to records of the first type encountered.
- The reason is that outputting mixed records is probably not what you want
- anyway, and you should remove all the unwanted records from the stream
- before outputting the table:
-\series bold
-grab
-\series default
- is your friend (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-grab"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to write a BED output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-BED"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Data in BED format can be output if the records contain the mandatory keys
- CHR, CHR_BEG, and CHR_END using
-\series bold
-write_bed
-\series default
-.
- If the optional keys are also present, they will be output as well:
-\end_layout
-
-\begin_layout LyX-Code
-write_bed --result_out=<file>
-\end_layout
-
-\begin_layout Subsection
-How to write PSL output?
-\begin_inset LatexCommand label
-name "sub:How-to-write-PSL"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Data in PSL format can be output using
-\series bold
-write_psl:
-\end_layout
-
-\begin_layout LyX-Code
-write_psl --result_out=<file>
-\end_layout
-
-\begin_layout Section
-Manipulating Records
-\end_layout
-
-\begin_layout Subsection
-How to select a few records?
-\begin_inset LatexCommand label
-name "sub:How-to-select-a-few-records"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-To quickly get an overview of your data you can limit the data stream to
- show a few records.
- This also very useful to test the pipeline with a few records if you are
- setting up a complex analysis using several biotools.
- That way you can inspect that all goes well before analyzing and waiting
- for the full data set.
- All of the read_<type> biotools have the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num switch which will take a number as argument and only that number of
- records will be read.
- So to read in the first 10 FASTA entries from a file:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna --num=10
-\end_layout
-
-\begin_layout Standard
-Another way of doing this is to use
-\series bold
-head_records
-\series default
- will limit the stream to show the first 10 records (default):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | head_records
-\end_layout
-
-\begin_layout Standard
-Using
-\series bold
-head_records
-\series default
- directly after one of the read_<type> biotools will be a lot slower than
- using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num switch with the read_<type> biotools, however,
-\series bold
-head_records
-\series default
- can also be used to limit the output from all the other biotools.
- It is also possible to give
-\series bold
-head_records
-\series default
- a number of records to show using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num switch.
- So to display the first 100 records do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | head_records --num=100
-\end_layout
-
-\begin_layout Subsection
-How to select random records?
-\begin_inset LatexCommand label
-name "sub:How-to-select-random-records"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-If you want to inspect a number of random records from the stream this can
- be done with the
-\series bold
-random_records
-\series default
- biotool.
- So if you have 1 mio records in the stream and you want to select 1000
- random records do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | random_records --num=1000
-\end_layout
-
-\begin_layout Subsection
-How to count all records in the data stream?
-\end_layout
-
-\begin_layout Standard
-To count all the records in the data stream use
-\series bold
-count_records
-\series default
-, which adds one record (which is not included in the count) to the data
- stream.
- So to count the number of sequences in a FASTA file you can do this:
-\end_layout
-
-\begin_layout LyX-Code
-cat test.fna | read_fasta | count_records --no_stream
-\end_layout
-
-\begin_layout Standard
-Which will write the last record containing the count to 'stdout':
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-count_records: 630
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
----
-\end_layout
-
-\begin_layout Standard
-It is also possible to write the count to file using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out switch.
-\end_layout
-
-\begin_layout Subsection
-How to get the length of record values?
-\begin_inset LatexCommand label
-name "sub:How-to-get-value_length"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Use the
-\series bold
-length_vals
-\series default
- biotool to get the length of each value for a comma separated list of keys:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | length_vals --keys=HIT,PATTERN
-\end_layout
-
-\begin_layout Subsection
-How to grab specific records?
-\begin_inset LatexCommand label
-name "sub:How-to-grab"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The biotool
-\series bold
-grab
-\series default
- is related to the Unix grep and locates records based on matching keys
- and/or values using either a pattern, a Perl regex, or a numerical evaluation.
- To easily
-\series bold
-grab
-\series default
- all records in the stream that has any mentioning of the pattern 'human'
- just pipe the data stream through
-\series bold
-grab
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human
-\end_layout
-
-\begin_layout Standard
-This will search for the pattern 'human' in all keys and all values.
- The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern switch takes a comma separated list of patterns, so in order to
- match multiple patterns do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human,mouse
-\end_layout
-
-\begin_layout Standard
-It is also possible to use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in switch instead of
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern.
-
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in is used to read a file with one pattern per line:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern_in=patterns.txt
-\end_layout
-
-\begin_layout Standard
-If you want the opposite result --- to find all records that does not match
- the patterns, add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-invert switch, which not only works with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern switch, but also with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-regex and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-eval:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human --invert
-\end_layout
-
-\begin_layout Standard
-If you want to search the record keys only,
-\emph on
-e.g.
-
-\emph default
- to find all records containing the key SEQ you can add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys_only switch.
- This will prevent matching of SEQ in any record value, and in fact SEQ
- is a not uncommon peptide sequence you could get an unwanted record.
- Also, this will give an increase in speed since only the keys are searched:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=SEQ --keys_only
-\end_layout
-
-\begin_layout Standard
-However, if you are interested in finding the peptide sequence SEQ and not
- the SEQ key, just add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-vals_only switch instead:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=SEQ --vals_only
-\end_layout
-
-\begin_layout Standard
-Also, if you want to grab for certain key/value pairs you can supply a comma
- separated list of keys whos values will then be searched using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-keys switch.
- This is handy if your records contain large genomic sequences and you dont
- want to search the entire sequence for
-\emph on
-e.g.
-
-\emph default
- the organism name --- it is much faster to tell
-\series bold
-grab
-\series default
- which keys to search the value for:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern=human --keys=SEQ_NAME
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout Standard
-It is also possible to invoke flexible matching using regex (regular expressions
-) instead of simple pattern matching.
- In
-\series bold
-grab
-\series default
- the regex engine is Perl based and allows use of different type of wild
- cards, alternatives,
-\emph on
-etc
-\emph default
-
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://perldoc.perl.org/perlreref.html"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-.
- If you want to
-\series bold
-grab
-\series default
- records withs the sequence ATCG or GCTA you can do this:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --regex='ATCG|GCTA'
-\end_layout
-
-\begin_layout Standard
-Or if you want to find sequences beginning with ATCG:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --regex='^ATCG'
-\end_layout
-
-\begin_layout Standard
-You can also use
-\series bold
-grab
-\series default
- to locate records that fulfill a numerical property using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-eval switch witch takes an expression in three parts.
- The first part is the key that holds the value we want to evaluate, the
- second part holds one the six operators:
-\end_layout
-
-\begin_layout Enumerate
-Greater than: >
-\end_layout
-
-\begin_layout Enumerate
-Greater than or equal to: >=
-\end_layout
-
-\begin_layout Enumerate
-Less than: <
-\end_layout
-
-\begin_layout Enumerate
-Less than or equal to: <=
-\end_layout
-
-\begin_layout Enumerate
-Equal to: =
-\end_layout
-
-\begin_layout Enumerate
-Not equal to: !=
-\end_layout
-
-\begin_layout Enumerate
-String wise equal to: eq
-\end_layout
-
-\begin_layout Enumerate
-String wise not equal to: ne
-\end_layout
-
-\begin_layout Standard
-And finally comes the number used in the evaluation.
- So to
-\series bold
-grab
-\series default
- all records with a sequence length greater than 30:
-\end_layout
-
-\begin_layout LyX-Code
-...
- length_seq | grab --eval='SEQ_LEN > 30'
-\end_layout
-
-\begin_layout Standard
-If you want to locate all records containing the pattern 'human' and where
- the sequence length is greater that 30, you do this by running the stream
- through
-\series bold
-grab
-\series default
- twice:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --pattern='human' | length_seq | grab --eval='SEQ_LEN > 30'
-\end_layout
-
-\begin_layout Standard
-Finally, it is possible to do fast matching of expressions from a file using
- the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-exact switch.
- Each of these expressions has to be matched exactly over the entrie length,
- which if useful if you have a file with accession numbers, that you want
- to locate in the stream:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | grab --exact acc_no.txt | ...
-\end_layout
-
-\begin_layout Standard
-Using
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-exact is much faster than using
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in, because with
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-exact the expression has to be complete matches, where
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in looks for subpatterns.
-\end_layout
-
-\begin_layout Standard
-NB! To get the best speed performance, use the most restrictive
-\series bold
-grab
-\series default
- first.
-\end_layout
-
-\begin_layout Subsection
-How to remove keys from records?
-\end_layout
-
-\begin_layout Standard
-To remove one or more specific keys from all records in the data stream
- use
-\series bold
-remove_keys
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | remove_keys --keys=SEQ,SEQ_NAME
-\end_layout
-
-\begin_layout Standard
-In the above example SEQ and SEQ_NAME will be removed from all records if
- they exists in these.
- If all keys are removed from a record, then the record will be removed.
-\end_layout
-
-\begin_layout Subsection
-How to rename keys in records?
-\end_layout
-
-\begin_layout Standard
-Sometimes you want to rename a record key,
-\emph on
-e.g.
-
-\emph default
- if you have read in a two column table with sequence name and sequence
- in each column (see
-\begin_inset LatexCommand ref
-reference "sub:How-to-read-table"
-
-\end_inset
-
-) without specifying the key names, then the sequence name will be called
- V0 and the sequence V1 as default in the
-\series bold
-read_tab
-\series default
- biotool.
- To rename the V0 and V1 keys we need to run the stream through
-\series bold
-rename_keys
-\series default
- twice (one for each key to rename):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | rename_keys --keys=V0,SEQ_NAME | rename_keys --keys=V1,SEQ
-\end_layout
-
-\begin_layout Standard
-The first instance of
-\series bold
-rename_keys
-\series default
- replaces all the V0 keys with SEQ_NAME, and the second instance of
-\series bold
-rename_keys
-\series default
- replaces all the V1 keys with SEQ.
-
-\emph on
-Et viola
-\emph default
- the data can now be used in the biotools that requires these keys.
-\end_layout
-
-\begin_layout Section
-Manipulating Sequences
-\end_layout
-
-\begin_layout Subsection
-How to get sequence lengths?
-\end_layout
-
-\begin_layout Standard
-The length for sequences in records can be determined with
-\series bold
-length_seq
-\series default
-, which adds the key SEQ_LEN to each record with the sequence length as
- the value.
- It also generates an extra record that is emitted last with the key TOTAL_SEQ_L
-EN showing the total length of all the sequences.
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_seq
-\end_layout
-
-\begin_layout Standard
-It is also possible to determine the sequence length using the generic tool
-
-\series bold
-length_vals
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-get-value_length"
-
-\end_inset
-
-, which determines the length of the values for a given list of keys:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_vals --keys=SEQ
-\end_layout
-
-\begin_layout Standard
-To obtain the total length of all sequences use
-\series bold
-sum_vals
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_vals --keys=SEQ
-\end_layout
-
-\begin_layout LyX-Code
-| sum_vals --keys=SEQ_LEN
-\end_layout
-
-\begin_layout Standard
-The biotool
-\series bold
-analyze_seq
-\series default
- will also determine the length of each sequence (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-analyze"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to analyze sequence composition?
-\begin_inset LatexCommand label
-name "sub:How-to-analyze"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-If you want to find out the sequence type, composition, length, as well
- as GC content, indel content and proportions of soft and hard masked sequence,
- then use
-\series bold
-analyze_seq
-\series default
-.
- This handy biotool will determine all these things per sequence from which
- it is easy to get an overview using the
-\series bold
-write_tab
-\series default
- biotool to output a table (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-tab"
-
-\end_inset
-
-).
- So in order to determine the sequence composition of a FASTA file with
- just one entry containing the sequence 'ATCG' we just read the data with
-
-\series bold
-read_fasta
-\series default
- and run the output through
-\series bold
-analyze_seq
-\series default
- which will add the analysis to the record like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq ...
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:D: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-MIX_INDEX: 0.55
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:W: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:G: 16
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SOFT_MASK%: 63.75
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:B: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:V: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-HARD_MASK%: 0.00
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:H: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:S: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:N: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:.: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-GC%: 35.00
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:A: 8
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:Y: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:M: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:T: 44
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SEQ_TYPE: DNA
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:K: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:~: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SEQ: TTTCAGTTTGGGACGGAGTAAGGCCTTCCtttttttttttttttttttttttttttttgagaccgagtcttgctc
-tgtcg
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-SEQ_LEN:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-80 RES:R: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:C: 12
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:-: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
-RES:U: 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\size scriptsize
----
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout Standard
-Now to make a table of how may As, Ts, Cs, and Gs you can add the following:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | analyze_seq | write_tab --keys=RES:A,RES:T,RES:C,RES:G
-\end_layout
-
-\begin_layout Standard
-Or if you want to see the proportions of hard and soft masked sequence:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | analyse_seq | write_tab --keys=HARD_MASK%,SOFT_MASK%
-\end_layout
-
-\begin_layout Standard
-If you have a stack of sequences in one file and you want to determine the
- mean GC content you can do it using the
-\series bold
-mean_vals
-\series default
- biotool:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq | mean_vals --keys=GC%
-\end_layout
-
-\begin_layout Standard
-Or if you want the total count of Ns you can use
-\series bold
-sum_vals
-\series default
- like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq | sum_vals --keys=RES:N
-\end_layout
-
-\begin_layout Standard
-The MIX_INDEX key is calculated as the count of the most common residue
- over the sequence length, and can be used as a cut-off for removing sequence
- tags consisting of mostly one nucleotide:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | analyze_seq | grab --eval='MIX_INDEX<0.85'
-\end_layout
-
-\begin_layout Subsection
-How to extract subsequences?
-\begin_inset LatexCommand label
-name "sub:How-to-extract"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-In order to extract a subsequence from a longer sequence use the biotool
- extract_seq, which will replace the sequence in the record with the subsequence
- (this behaviour should probably be modified to be dependant of a
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-replace or a
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_replace switch
-\begin_inset Note Note
-status collapsed
-
-\begin_layout Standard
-also in split_seq
-\end_layout
-
-\end_inset
-
-).
- So to extract the first 20 residues from all sequences do (first residue
- is designated 1):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | extract_seq --beg=1 --len=20
-\end_layout
-
-\begin_layout Standard
-You can also specify a begin and end coordinate set:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | extract_seq --beg=20 --end=40
-\end_layout
-
-\begin_layout Standard
-If you want the subsequences from position 20 to the sequence end do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | extract_seq --beg=20
-\end_layout
-
-\begin_layout Standard
-If you want to extract subsequences a given distance from the sequence end
- you can do this by reversing the sequence with the biotool
-\series bold
-reverse_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-reverse-seq"
-
-\end_inset
-
-, followed by
-\series bold
-extract_seq
-\series default
- to get the subsequence, and then
-\series bold
-reverse_seq
-\series default
- again to get the subsequence back in the original orientation:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=test.fna | reverse_seq
-\end_layout
-
-\begin_layout LyX-Code
-| extract_seq --beg=10 --len=10 | reverse_seq
-\end_layout
-
-\begin_layout Subsection
-How to get genomic sequence?
-\begin_inset LatexCommand label
-name "sub:How-to-get-genomic-sequence"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The biotool
-\series bold
-get_genomic_seq
-\series default
- can extract subsequences for a given genome specified with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-genome switch explicitly using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-beg and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-end/
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-len switches:
-\end_layout
-
-\begin_layout LyX-Code
-get_genome_seq --genome=<genome> --beg=1 --len=100
-\end_layout
-
-\begin_layout Standard
-Alternatively,
-\series bold
-get_genome_seq
-\series default
- can be used to append the corresponding sequence to BED, PSL, and BLAST
- records:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<BED file> | get_genome_seq --genome=<genome>
-\end_layout
-
-\begin_layout Standard
-It is also possible to include flaking sequence using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-flank switch.
- So to include 50 nucleotides upstream and 50 nucleotides downstream for
- each BED entry do:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<BED file> | get_genome_seq --genome=<genome> --flank=50
-\end_layout
-
-\begin_layout Subsection
-How to upper-case sequences?
-\end_layout
-
-\begin_layout Standard
-Sequences can be shifted from lower case to upper case using
-\series bold
-uppercase_seq
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | uppercase_seq
-\end_layout
-
-\begin_layout Subsection
-How to reverse sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-reverse-seq"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The order of residues in a sequence can be reversed using reverse_seq:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | reverse_seq
-\end_layout
-
-\begin_layout Standard
-Note that in order to reverse/complement a sequence you also need the
-\series bold
-complement_seq
-\series default
- biotool (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-complement"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to complement sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-complement"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-DNA and RNA sequences can be complemented with
-\series bold
-complement_seq
-\series default
-, which automagically determines the sequence type:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | complement_seq
-\end_layout
-
-\begin_layout Standard
-Note that in order to reverse/complement a sequence you also need the
-\series bold
-reverse_seq
-\series default
- biotool (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-reverse-seq"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to remove indels from sequnces?
-\end_layout
-
-\begin_layout Standard
-Indels can be removed from sequences with the
-\series bold
-remove_indels
-\series default
- biotool.
- This is useful if you have aligned some sequences (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-align"
-
-\end_inset
-
-) and extracted (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-extract"
-
-\end_inset
-
-) a block of subsequences from the alignment and you want to use these sequence
- in a search where you need to remove the indels first.
- '-', '~', and '.' are considered indels:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | remove_indels
-\end_layout
-
-\begin_layout Subsection
-How to shuffle sequences?
-\end_layout
-
-\begin_layout Standard
-All residues in sequences in the stream can be shuffled to random positions
- using the
-\series bold
-shuffle_seq
-\series default
- biotool:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | shuffle_seq
-\end_layout
-
-\begin_layout Subsection
-How to split sequences into overlapping subsequences?
-\end_layout
-
-\begin_layout Standard
-Sequences can be slit into overlapping subsequences with the
-\series bold
-split_seq
-\series default
- biotool.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | split_seq --word_size=20 --uniq
-\end_layout
-
-\begin_layout Subsection
-How to determine the oligo frequency?
-\end_layout
-
-\begin_layout Standard
-In order to determine if any oligo usage is over represented in one or more
- sequences you can determine the frequency of oligos of a given size with
-
-\series bold
-oligo_freq
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | oligo_freq --word_size=4
-\end_layout
-
-\begin_layout Standard
-And if you have more than one sequence and want to accumulate the frequences
- you need the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-all switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | oligo_freq --word_size=4 --all
-\end_layout
-
-\begin_layout Standard
-To get a meaningful result you need to write the resulting frequencies as
- a table with
-\series bold
-write_tab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-tab"
-
-\end_inset
-
-), but first it is important to
-\series bold
-grab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-grab"
-
-\end_inset
-
-) the records with the frequencies to avoid full length sequences in the
- table:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | oligo_freq --word_size=4 --all | grab --pattern=OLIGO --keys_only
-\end_layout
-
-\begin_layout LyX-Code
-| write_tab --no_stream
-\end_layout
-
-\begin_layout Standard
-And the resulting frequency table can be sorted with Unix sort (man sort).
-\end_layout
-
-\begin_layout Subsection
-How to search for sequences in genomes?
-\end_layout
-
-\begin_layout Standard
-See the following biotool:
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-patscan_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-patscan"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-blat_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAT"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-blast_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAST"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-
-\series bold
-vmatch_seq
-\series default
-
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-Vmatch"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to search sequences for a pattern?
-\begin_inset LatexCommand label
-name "sub:How-to-use-patscan"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-It is possible to search sequences in the data stream for patterns using
- the
-\series bold
-patscan_seq
-\series default
- biotool which utilizes the powerful scan_for_matches engine.
- Consult the documentation for scan_for_matches in order to learn how to
- define patterns (the documentation is included in Appendix\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sec:scan_for_matches-README"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Standard
-To search all sequences for a simple pattern consisting of the sequence
- ATCGATCG allowing for 3 mismatches, 2 insertions and 1 deletion:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | patscan_seq --pattern='ATCGATCG[3,2,1]'
-\end_layout
-
-\begin_layout Standard
-The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern switch takes a comma seperated list of patterns, so if you want
- to search for more that one pattern do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern='ATCGATCG[3,2,1],GCTAGCTA[3,2,1]'
-\end_layout
-
-\begin_layout Standard
-It is also possible to have a list of different patterns to search for in
- a file with one pattern per line.
- In order to get
-\series bold
-patscan_seq
-\series default
- to read these patterns use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-pattern_in switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern_in=<file>
-\end_layout
-
-\begin_layout Standard
-To also scan the complementary strand in nucleotide sequences (
-\series bold
-patscan_seq
-\series default
- automagically determines the sequence type) you need to add the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-comp switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern=<pattern> --comp
-\end_layout
-
-\begin_layout Standard
-It is also possible to use
-\series bold
-patscan_seq
-\series default
- to output those records that does not contain a certain pattern by using
- the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-invert switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | patscan_seq --pattern=<pattern> --invert
-\end_layout
-
-\begin_layout Standard
-Finally,
-\series bold
-patscan_seq
-\series default
- can also scan for patterns in a given genome sequence, instead of sequences
- in the stream, using the
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-genome switch:
-\end_layout
-
-\begin_layout LyX-Code
-patscan --pattern=<pattern> --genome=<genome>
-\end_layout
-
-\begin_layout Subsection
-How to use BLAT for sequence search?
-\begin_inset LatexCommand label
-name "sub:How-to-use-BLAT"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Sequences in the data stream can be matched against supported genomes using
-
-\series bold
-blat_seq
-\series default
- which is a biotool using BLAT as the name might suggest.
- Currently only Mouse and Human genomes are available and it is not possible
- to use OOC files since there is still a need for a local repository for
- genome files.
- Otherwise it is just:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | blat_seq --genome=<genome>
-\end_layout
-
-\begin_layout Standard
-The search results can then be written to file with
-\series bold
-write_psl
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-PSL"
-
-\end_inset
-
-) or
-\series bold
-write_bed
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-BED"
-
-\end_inset
-
-) allthough with
-\series bold
-write_bed
-\series default
- some information will be lost).
- It is also possible to plot chromosome distribution of the search results
- using
-\series bold
-plot_chrdist
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-plot-chrdist"
-
-\end_inset
-
-) or the distribution of the match lengths using
-\series bold
-plot_lendist
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-plot-lendist"
-
-\end_inset
-
-) or a karyogram with the hits using
-\series bold
-plot_karyogram
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-plot-karyogram"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to use BLAST for sequence search?
-\begin_inset LatexCommand label
-name "sub:How-to-use-BLAST"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Two biotools exist for blasting sequences:
-\series bold
-create_blast_db
-\series default
- is used to create the BLAST database required for BLAST which is queried
- using the biotool
-\series bold
-blast_seq
-\series default
-.
- So in order to create a BLAST database from sequences in the data stream
- you simple run:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_blast_db --database=my_database --no_stream
-\end_layout
-
-\begin_layout Standard
-The type of sequence to use for the database is automagically determined
- by
-\series bold
-create_blast_db
-\series default
-, but don't have a mixture of peptide and nucleic acids sequences in the
- stream.
- The
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-database switch takes a path as argument, but will default to 'blastdb_<time_sta
-mp> if not set.
-\end_layout
-
-\begin_layout Standard
-The resulting database can now be queried with sequences in another data
- stream using
-\series bold
-blast_seq
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | blast_seq --database=my_database
-\end_layout
-
-\begin_layout Standard
-Again, the sequence type is determined automagically and the appropriate
- BLAST program is guessed (see below table), however, the program name can
- be overruled with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-program switch.
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Tabular
-<lyxtabular version="3" rows="5" columns="3">
-<features>
-<column alignment="center" valignment="top" width="0">
-<column alignment="center" valignment="top" width="0">
-<column alignment="center" valignment="top" width="0">
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Subject sequence
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Query sequence
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Program guess
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-blastn
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-blastp
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-blastx
-\end_layout
-
-\end_inset
-</cell>
-</row>
-<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Nucleotide
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-Protein
-\end_layout
-
-\end_inset
-</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
-\begin_inset Text
-
-\begin_layout Standard
-tblastn
-\end_layout
-
-\end_inset
-</cell>
-</row>
-</lyxtabular>
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Finally, it is also possible to use
-\series bold
-blast_seq
-\series default
- for blasting sequences agains a preformatted genome using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-genome switch instead of the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-database switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | blast_seq --genome=<genome>
-\end_layout
-
-\begin_layout Subsection
-How to use Vmatch for sequence search?
-\begin_inset LatexCommand label
-name "sub:How-to-use-Vmatch"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The powerful suffix array software package Vmatch
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://www.vmatch.de/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
- can be used for exact mapping of sequences against indexed genomes using
- the biotool
-\series bold
-vmatch_seq
-\series default
-, which will e.g.
- map 700000 ESTs to the human genome locating all 160 mio hits in less than
- an hour.
- Only nucleotide sequences and sequences longer than 11 nucleotides will
- be mapped.
- It is recommended that sequences consisting of mostly one nucleotide type
- are removed.
- This can be done with the
-\series bold
-analyze_seq
-\series default
- biotool
-\begin_inset LatexCommand eqref
-reference "sub:How-to-analyze"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome>
-\end_layout
-
-\begin_layout Standard
-It is also possible to allow for mismatches using the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-hamming_dist switch.
- So to allow for 2 mismatches:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=2
-\end_layout
-
-\begin_layout Standard
-Or to allow for 10% mismathing nucleotides:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=10p
-\end_layout
-
-\begin_layout Standard
-To allow both indels and mismatches use the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-edit_dist switch.
- So to allow for one mismatch or one indel:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=1
-\end_layout
-
-\begin_layout Standard
-Or to allow for 5% indels or mismatches:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | vmatch_seq --genome=<genome> --hamming_dist=5p
-\end_layout
-
-\begin_layout Standard
-Note that using
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-hamming_dist or
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-edit_dist greatly slows down vmatch considerably --- use with care.
-\end_layout
-
-\begin_layout Standard
-The resulting SCORE key can be replaced to hold the number of genome matches
- of a given sequence (multi-mappers) is the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-count switch is given.
-\end_layout
-
-\begin_layout Subsection
-How to find all matches between sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-find-matches"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-All matches between two sequences can be determined with the biotool
-\series bold
-match_seq
-\series default
-.
- The match finding engine underneath the hood of
-\series bold
-match_seq
-\series default
- is the super fast suffix tree program MUMmer
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://mummer.sourceforge.net/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-, which will locate all forward and reverse matches between huge sequences
- in a matter of minutes (if the repeat count is not too high and if the
- word size used is appropriate).
- Matching two
-\emph on
-Helicobacter pylori
-\emph default
- genomes (1.7Mbp) takes around 10 seconds:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | match_seq --word_size=20 --direction=both
-\end_layout
-
-\begin_layout Standard
-The output from
-\series bold
-match_seq
-\series default
- can be used to generate a dot plot with
-\series bold
-plot_matches
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-generate-dotplot"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to align sequences?
-\begin_inset LatexCommand label
-name "sub:How-to-align"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Sequences in the stream can be aligned with the
-\series bold
-align_seq
-\series default
- biotool that uses Muscle
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://www.drive5.com/muscle/muscle.html"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
- as aligment engine.
- Currently you cannot change any of the Muscle alignment parameters and
-
-\series bold
-align_seq
-\series default
- will create an alignment based on the defaults (which are really good!):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | align_seq
-\end_layout
-
-\begin_layout Standard
-The aligned output can be written to file in FASTA format using
-\series bold
-write_fasta
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-fasta"
-
-\end_inset
-
-) or in pretty text using
-\series bold
-write_align
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-alignment"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-How to create a weight matrix?
-\end_layout
-
-\begin_layout Standard
-If you want a weight matrix to show the sequence composition of a stack
- of sequences you can use the biotool create_weight_matrix:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_weight_matrix
-\end_layout
-
-\begin_layout Standard
-The result can be output in percent using the
-\begin_inset ERT
-status open
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-percent switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_weight_matrix --percent
-\end_layout
-
-\begin_layout Standard
-The weight matrix can be written as tabular output with
-\series bold
-write_tab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-tab"
-
-\end_inset
-
-) after removeing the records containing SEQ with
-\series bold
-grab
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-grab"
-
-\end_inset
-
-):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | create_weight_matrix | grab --invert --keys=SEQ --keys_only
-\end_layout
-
-\begin_layout LyX-Code
-| write_tab --no_stream
-\end_layout
-
-\begin_layout Standard
-The V0 column will hold the residue, while the rest of the columns will
- hold the frequencies for each sequence position.
-\end_layout
-
-\begin_layout Section
-Plotting
-\end_layout
-
-\begin_layout Standard
-There exists several biotools for plotting.
- Some of these are based on GNUplot
-\begin_inset Foot
-status open
-
-\begin_layout Standard
-\begin_inset LatexCommand url
-target "http://www.gnuplot.info/"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-, which is an extremely powerful platform to generate all sorts of plots
- and even though GNUplot has quite a steep learning curve, the biotools
- utilizing GNUplot are simple to use.
- GNUplot is able to output a lot of different formats (called terminals
- in GNUplot), but the biotools focusses on three formats only:
-\end_layout
-
-\begin_layout Enumerate
-The 'dumb' terminal is default to the GNUplot based biotools and will output
- a plot in crude ASCII text (Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Dumb-terminal"
-
-\end_inset
-
-).
- This is quite nice for a quick and dirty plot to get an overview of your
- data .
-\end_layout
-
-\begin_layout Enumerate
-The 'post' or 'postscript' terminal output postscript code which is publication
- grade graphics that can be viewed with applications such as Ghostview,
- Photoshop, and Preview.
-\end_layout
-
-\begin_layout Enumerate
-The 'svg' terminal output's scalable vector graphics (SVG) which is a vector
- based format.
- SVG is great because you can edit the resulting plot using Photoshop or
- Inkscape
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-Inkscape is a really handy drawing program that is free and open source.
- Availble at
-\begin_inset LatexCommand htmlurl
-target "http://www.inkscape.org"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
- if you want to add additional labels, captions, arrows, and so on and then
- save the result in different formats, such as postscript without loosing
- resolution.
-\end_layout
-
-\begin_layout Standard
-The biotools for plotting that are not based on GNUplot only output SVG
- (that may change in the future).
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename lendist_ascii.png
- lyxscale 70
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Dumb-terminal"
-
-\end_inset
-
-Dumb terminal
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-The output of a length distribution plot in the default 'dumb terminal'
- to the terminal window.
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a histogram?
-\begin_inset LatexCommand label
-name "How-to-plot-histogram"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-A generic histogram for a given value can be plotted with the biotool
-\series bold
-plot_histogram
-\series default
- (Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Histogram"
-
-\end_inset
-
-):
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_histogram --key=TISSUE --no_stream
-\end_layout
-
-\begin_layout Standard
-(Figure missing)
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align left
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename histogram.png
- lyxscale 70
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Histogram"
-
-\end_inset
-
-Histogram
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a length distribution?
-\begin_inset LatexCommand label
-name "sub:How-to-plot-lendist"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Plotting of length distributions, weather sequence lengths, patterns lengths,
- hit lengths,
-\emph on
-etc.
-
-\emph default
- is a really handy thing and can be done with the the biotool
-\series bold
-plot_lendist
-\series default
-.
- If you have a file with FASTA entries and want to plot the length distribution
- you do it like this:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | length_seq
-\end_layout
-
-\begin_layout LyX-Code
-| plot_lendist --key=SEQ_LEN --no_stream
-\end_layout
-
-\begin_layout Standard
-The result will be written to the default dumb terminal and will look like
- Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Dumb-terminal"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-If you instead want the result in postscript format you can do:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_lendist --key=SEQ_LEN --terminal=post --result_out=file.ps
-\end_layout
-
-\begin_layout Standard
-That will generate the plot and save it to file, but not interrupt the data
- stream which can then be used in further analysis.
- You can also save the plot implicetly using '>', however, it is then important
- to terminate the stream with the
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream switch:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_lendist --key=SEQ_LEN --terminal=post --no_stream > file.ps
-\end_layout
-
-\begin_layout Standard
-The resulting plot can be seen in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Length-distribution"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename lendist.ps
- lyxscale 50
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Length-distribution"
-
-\end_inset
-
-Length distribution
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-Length distribution of 630 piRNA like RNAs.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a chromosome distribution?
-\begin_inset LatexCommand label
-name "sub:How-to-plot-chrdist"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-If you have the result of a sequence search against a multi chromosome genome,
- it is very practical to be able to plot the distribution of search hits
- on the different chromosomes.
- This can be done with
-\series bold
-plot_chrdist
-\series default
-:
-\end_layout
-
-\begin_layout LyX-Code
-read_fasta --data_in=<file> | blat_genome | plot_chrdist --no_stream
-\end_layout
-
-\begin_layout Standard
-The above example will result in a crude plot using the 'dumb' terminal,
- and if you want to mess around with the results from the BLAT search you
- probably want to save the result to file first (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-write-PSL"
-
-\end_inset
-
-).
- To plot the chromosome distribution from the saved search result you can
- do:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=file.bed | plot_chrdist --terminal=post --result_out=plot.ps
-\end_layout
-
-\begin_layout Standard
-That will result in the output show in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Chromosome-distribution"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename chrdist.ps
- lyxscale 50
- width 12cm
- rotateAngle 90
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Chromosome-distribution"
-
-\end_inset
-
-Chromosome distribution
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to generate a dotplot?
-\begin_inset LatexCommand label
-name "sub:How-to-generate-dotplot"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-A dotplot is a powerful way to get an overview of the size and location
- of sequence insertions, deletions, and duplications between two sequences.
- Generating a dotplot with biotools is a two step process where you initially
- find all matches between two sequences using the tool
-\series bold
-match_seq
-\series default
- (see\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "sub:How-to-find-matches"
-
-\end_inset
-
-) and plot the resulting matches with
-\series bold
-plot_matches
-\series default
-.
- Matching and plotting two
-\emph on
-Helicobacter pylori
-\emph default
- genomes (1.7Mbp) takes around 10 seconds:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | match_seq | plot_matches --terminal=post --result_out=plot.ps
-\end_layout
-
-\begin_layout Standard
-The resulting dotplot is in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Dotplot"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename dotplot.ps
- lyxscale 50
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Dotplot"
-
-\end_inset
-
-Dotplot
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-Forward matches are displayed in green while reverse matches are displayed
- in red.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a sequence logo?
-\end_layout
-
-\begin_layout Standard
-Sequence logos can be generate with
-\series bold
-plot_seqlogo
-\series default
-.
- The sequnce type is determined automagically and an entropy scale of 2
- bits and 4 bits is used for nucleotide and peptide sequences, respectively
-\begin_inset Foot
-status collapsed
-
-\begin_layout Standard
-\begin_inset LatexCommand htmlurl
-target "http://www.ccrnp.ncifcrf.gov/~toms/paper/hawaii/latex/node5.html"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_seqlogo --no_stream --result_out=seqlogo.svg
-\end_layout
-
-\begin_layout Standard
-An example of a sequence logo can be seen in Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Sequence-logo"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename seqlogo.png
- lyxscale 50
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Sequence-logo"
-
-\end_inset
-
-Sequence logo
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-How to plot a karyogram?
-\begin_inset LatexCommand label
-name "sub:How-to-plot-karyogram"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-To plot search hits on genomes use
-\series bold
-plot_karyogram
-\series default
-, which will output a nice karyogram in SVG graphics:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | plot_karyogram --result_out=karyogram.svg
-\end_layout
-
-\begin_layout Standard
-The banding data is taken from the UCSC genome browser database and currently
- only Human and Mouse is supported.
- Fig.\InsetSpace ~
-
-\begin_inset LatexCommand ref
-reference "fig:Karyogram"
-
-\end_inset
-
- shows the distribution of piRNA like RNAs matched to the Human genome.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename karyogram.png
- lyxscale 35
- width 12cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:Karyogram"
-
-\end_inset
-
-Karyogram
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Quote
-Hits from a search of piRNA like RNAs in the Human genome is displayed as
- short horizontal bars.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Section
-Uploading Results
-\end_layout
-
-\begin_layout Subsection
-How do I display my results in the UCSC Genome Browser?
-\end_layout
-
-\begin_layout Standard
-Results from the list of biotools below can be uploaded directly to a local
- mirror of the UCSC Genome Browser using the biotool
-\series bold
-upload_to_ucsc
-\series default
-:
-\end_layout
-
-\begin_layout Itemize
-patscan_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-patscan"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-blat_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAT"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-blast_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-BLAST"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-vmatch_seq
-\begin_inset LatexCommand eqref
-reference "sub:How-to-use-Vmatch"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The syntax for uploading data the most simple way requires two mandatory
- switches:
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-database, which is the UCSC database name (such as hg18, mm9, etc.) and
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-table which should be the users initials followed by an underscore and a
- short description of the data:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | upload_to_ucsc --database=hg18 --table=mah_snoRNAs
-\end_layout
-
-\begin_layout Standard
-The
-\series bold
-upload_to_ucsc
-\series default
- biotool modifies the users ~/ucsc/my_tracks.ra file automagically (a backup
- is created with the name ~/ucsc/my_tracks.ra~) with default values that
- can be overridden using the following switches:
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-short_label - Short label for track - Default=database->table
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-long_label - Long label for track - Default=database->table
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-group - Track group name - Default=<user name as defined in env>
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-priority - Track display priority - Default=1
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-color - Track color - Default=147,73,42
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-chunk_size - Chunks for loading - Default=10000000
-\end_layout
-
-\begin_layout Itemize
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-visibility - Track visibility - Default=pack
-\end_layout
-
-\begin_layout Standard
-Also, data in BED or PSL format can be uploaded with
-\series bold
-upload_to_ucsc
-\series default
- as long as these reference to genomes and chromosomes existing in the UCSC
- Genome Browser:
-\end_layout
-
-\begin_layout LyX-Code
-read_bed --data_in=<bed file> | upload_to_ucsc ...
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-read_psl --data_in=<psl file> | upload_to_ucsc ...
-\end_layout
-
-\begin_layout Section
-Power Scripting
-\end_layout
-
-\begin_layout Standard
-It is possible to do commandline scripting of biotool records using Perl.
- Because a biotool record essentially is a hash structure, you can pass
- records to
-\series bold
-bioscript
-\series default
- command, which is a wrapper around the Perl executable that allows direct
- manipulations of the records using the power of Perl.
-\end_layout
-
-\begin_layout Standard
-In the below example we replace in all records the value to the CHR key
- with a forthrunning number:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | bioscript 'while($r=get_record(
-\backslash
-*STDIN)){$r->{CHR}=$i++; put_record($r)}'
-\end_layout
-
-\begin_layout Standard
-Something more useful would probably be to create custom FASTA headers.
- E.g.
- if we read in a BED file, lookup the genomic sequence, create a custom
- FASTA header with
-\series bold
-bioscript
-\series default
- and output FASTA entries:
-\end_layout
-
-\begin_layout LyX-Code
-...
- | bioscript 'while($r=get_record(
-\backslash
-*STDIN)){$r->{SEQ_NAME}= //
-\end_layout
-
-\begin_layout LyX-Code
-join("_",$r->{CHR},$r->{CHR_BEG},$r->{CHR_END}); put_record($r)}'
-\end_layout
-
-\begin_layout Standard
-And the output:
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_21567527_21567550
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_693380_693403
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_13859534_13859557
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_9005090_9005113
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_2106825_2106848
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout LyX-Code
->chr2L_14649031_14649054
-\end_layout
-
-\begin_layout LyX-Code
-taccaaacggatgcctcagacatc
-\end_layout
-
-\begin_layout Section
-Trouble shooting
-\end_layout
-
-\begin_layout Standard
-Shoot the messenger!
-\end_layout
-
-\begin_layout Section
-\start_of_appendix
-Keys
-\begin_inset LatexCommand label
-name "sec:Keys"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-HIT
-\end_layout
-
-\begin_layout Standard
-HIT_BEG
-\end_layout
-
-\begin_layout Standard
-HIT_END
-\end_layout
-
-\begin_layout Standard
-HIT_LEN
-\end_layout
-
-\begin_layout Standard
-HIT_NAME
-\end_layout
-
-\begin_layout Standard
-PATTERN
-\end_layout
-
-\begin_layout Section
-Switches
-\begin_inset LatexCommand label
-name "sec:Switches"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_in
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-stream_out
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-no_stream
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-data_in
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-result_out
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
--
-\backslash
-/-
-\end_layout
-
-\end_inset
-
-num
-\end_layout
-
-\begin_layout Section
-scan_for_matches README
-\begin_inset LatexCommand label
-name "sec:scan_for_matches-README"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches:
-\end_layout
-
-\begin_layout LyX-Code
- A Program to Scan Nucleotide or Protein Sequences for Matching Patterns
-\end_layout
-
-\begin_layout LyX-Code
- Ross Overbeek
-\end_layout
-
-\begin_layout LyX-Code
- MCS
-\end_layout
-
-\begin_layout LyX-Code
- Argonne National Laboratory
-\end_layout
-
-\begin_layout LyX-Code
- Argonne, IL 60439
-\end_layout
-
-\begin_layout LyX-Code
- USA
-\end_layout
-
-\begin_layout LyX-Code
-Scan_for_matches is a utility that we have written to search for
-\end_layout
-
-\begin_layout LyX-Code
-patterns in DNA and protein sequences.
- I wrote most of the code,
-\end_layout
-
-\begin_layout LyX-Code
-although David Joerg and Morgan Price wrote sections of an
-\end_layout
-
-\begin_layout LyX-Code
-earlier version.
- The whole notion of pattern matching has a rich
-\end_layout
-
-\begin_layout LyX-Code
-history, and we borrowed liberally from many sources.
- However, it is
-\end_layout
-
-\begin_layout LyX-Code
-worth noting that we were strongly influenced by the elegant tools
-\end_layout
-
-\begin_layout LyX-Code
-developed and distributed by David Searls.
- My intent is to make the
-\end_layout
-
-\begin_layout LyX-Code
-existing tool available to anyone in the research community that might
-\end_layout
-
-\begin_layout LyX-Code
-find it useful.
- I will continue to try to fix bugs and make suggested
-\end_layout
-
-\begin_layout LyX-Code
-enhancements, at least until I feel that a superior tool exists.
-\end_layout
-
-\begin_layout LyX-Code
-Hence, I would appreciate it if all bug reports and suggestions are
-\end_layout
-
-\begin_layout LyX-Code
-directed to me at Overbeek@mcs.anl.gov.
-
-\end_layout
-
-\begin_layout LyX-Code
-I will try to log all bug fixes and report them to users that send me
-\end_layout
-
-\begin_layout LyX-Code
-their email addresses.
- I do not require that you give me your name
-\end_layout
-
-\begin_layout LyX-Code
-and address.
- However, if you do give it to me, I will try to notify
-\end_layout
-
-\begin_layout LyX-Code
-you of serious problems as they are discovered.
-\end_layout
-
-\begin_layout LyX-Code
-Getting Started:
-\end_layout
-
-\begin_layout LyX-Code
- The distribution should contain at least the following programs:
-\end_layout
-
-\begin_layout LyX-Code
- README - This document
-\end_layout
-
-\begin_layout LyX-Code
- ggpunit.c - One of the two source files
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches.c - The second source file
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- run_tests - A perl script to test things
-\end_layout
-
-\begin_layout LyX-Code
- show_hits - A handy perl script
-\end_layout
-
-\begin_layout LyX-Code
- test_dna_input - Test sequences for DNA
-\end_layout
-
-\begin_layout LyX-Code
- test_dna_patterns - Test patterns for DNA scan
-\end_layout
-
-\begin_layout LyX-Code
- test_output - Desired output from test
-\end_layout
-
-\begin_layout LyX-Code
- test_prot_input - Test protein sequences
-\end_layout
-
-\begin_layout LyX-Code
- test_prot_patterns - Test patterns for proteins
-\end_layout
-
-\begin_layout LyX-Code
- testit - a perl script used for test
-\end_layout
-
-\begin_layout LyX-Code
- Only the first three files are required.
- The others are useful,
-\end_layout
-
-\begin_layout LyX-Code
- but only if you have Perl installed on your system.
- If you do
-\end_layout
-
-\begin_layout LyX-Code
- have Perl, I suggest that you type
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- which perl
-\end_layout
-
-\begin_layout LyX-Code
- to find out where it installed.
- On my system, I get the following
-\end_layout
-
-\begin_layout LyX-Code
- response:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- clone% which perl
-\end_layout
-
-\begin_layout LyX-Code
- /usr/local/bin/perl
-\end_layout
-
-\begin_layout LyX-Code
- indicating that Perl is installed in /usr/local/bin.
- Anyway, once
-\end_layout
-
-\begin_layout LyX-Code
- you know where it is installed, edit the first line of files
-\end_layout
-
-\begin_layout LyX-Code
- testit
-\end_layout
-
-\begin_layout LyX-Code
- show_hits
-\end_layout
-
-\begin_layout LyX-Code
- replacing /usr/local/bin/perl with the appropriate location.
- I
-\end_layout
-
-\begin_layout LyX-Code
- will assume that you can do this, although it is not critical (it
-\end_layout
-
-\begin_layout LyX-Code
- is needed only to test the installation and to use the "show_hits"
-\end_layout
-
-\begin_layout LyX-Code
- utility).
- Perl is not required to actually install and run
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches.
-
-\end_layout
-
-\begin_layout LyX-Code
- If you do not have Perl, I suggest you get it and install it (it
-\end_layout
-
-\begin_layout LyX-Code
- is a wonderful utility).
- Information about Perl and how to get it
-\end_layout
-
-\begin_layout LyX-Code
- can be found in the book "Programming Perl" by Larry Wall and
-\end_layout
-
-\begin_layout LyX-Code
- Randall L.
- Schwartz, published by O'Reilly & Associates, Inc.
-\end_layout
-
-\begin_layout LyX-Code
- To get started, you will need to compile the program.
- I do this
-\end_layout
-
-\begin_layout LyX-Code
- using
-\end_layout
-
-\begin_layout LyX-Code
- gcc -O -o scan_for_matches ggpunit.c scan_for_matches.c
-\end_layout
-
-\begin_layout LyX-Code
- If you do not use GNU C, use
-\end_layout
-
-\begin_layout LyX-Code
- cc -O -DCC -o scan_for_matches ggpunit.c scan_for_matches.c
-\end_layout
-
-\begin_layout LyX-Code
- which works on my Sun.
-
-\end_layout
-
-\begin_layout LyX-Code
- Once you have compiled scan_for_matches, you can verify that it
-\end_layout
-
-\begin_layout LyX-Code
- works with
-\end_layout
-
-\begin_layout LyX-Code
- clone% run_tests tmp
-\end_layout
-
-\begin_layout LyX-Code
- clone% diff tmp test_output
-\end_layout
-
-\begin_layout LyX-Code
- You may get a few strange lines of the sort
-\end_layout
-
-\begin_layout LyX-Code
- clone% run_tests tmp
-\end_layout
-
-\begin_layout LyX-Code
- rm: tmp: No such file or directory
-\end_layout
-
-\begin_layout LyX-Code
- clone% diff tmp test_output
-\end_layout
-
-\begin_layout LyX-Code
- These should cause no concern.
- However, if the "diff" shows that
-\end_layout
-
-\begin_layout LyX-Code
- tmp and test_output are different, contact me (you have a
-\end_layout
-
-\begin_layout LyX-Code
- problem).
-
-\end_layout
-
-\begin_layout LyX-Code
- You should now be able to use scan_for_matches by following the
-\end_layout
-
-\begin_layout LyX-Code
- instructions given below (which is all the normal user should have
-\end_layout
-
-\begin_layout LyX-Code
- to understand, once things are installed properly).
-\end_layout
-
-\begin_layout LyX-Code
- ==============================================================
-\end_layout
-
-\begin_layout LyX-Code
-How to run scan_for_matches:
-\end_layout
-
-\begin_layout LyX-Code
- To run the program, you type need to create two files
-\end_layout
-
-\begin_layout LyX-Code
- 1.
- the first file contains the pattern you wish to scan for; I'll
-\end_layout
-
-\begin_layout LyX-Code
- call this file pat_file in what follows (but any name is ok)
-\end_layout
-
-\begin_layout LyX-Code
- 2.
- the second file contains a set of sequences to scan.
- These
-\end_layout
-
-\begin_layout LyX-Code
- should be in "fasta format".
- Just look at the contents of
-\end_layout
-
-\begin_layout LyX-Code
- test_dna_input to see examples of this format.
- Basically,
-\end_layout
-
-\begin_layout LyX-Code
- each sequence begins with a line of the form
-\end_layout
-
-\begin_layout LyX-Code
- >sequence_id
-\end_layout
-
-\begin_layout LyX-Code
- and is followed by one or more lines containing the sequence.
-\end_layout
-
-\begin_layout LyX-Code
- Once these files have been created, you just use
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches pat_file < input_file
-\end_layout
-
-\begin_layout LyX-Code
- to scan all of the input sequences for the given pattern.
- As an
-\end_layout
-
-\begin_layout LyX-Code
- example, suppose that pat_file contains a single line of the form
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...7 3...8 ~p1
-\end_layout
-
-\begin_layout LyX-Code
- Then,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- should produce two "hits".
- When I run this on my machine, I get
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[6,27]
-\end_layout
-
-\begin_layout LyX-Code
- cguaacc ggttaacc gguuacg
-\end_layout
-
-\begin_layout LyX-Code
- >tst2:[6,27]
-\end_layout
-
-\begin_layout LyX-Code
- CGUAACC GGTTAACC GGUUACG
-\end_layout
-
-\begin_layout LyX-Code
- clone%
-\end_layout
-
-\begin_layout LyX-Code
-Simple Patterns Built by Matching Ranges and Reverse Complements
-\end_layout
-
-\begin_layout LyX-Code
- Let me first explain this simple pattern:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...7 3...8 ~p1
-\end_layout
-
-\begin_layout LyX-Code
- The pattern consists of three "pattern units" separated by spaces.
-\end_layout
-
-\begin_layout LyX-Code
- The first pattern unit is
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...7
-\end_layout
-
-\begin_layout LyX-Code
- which means "match 4 to 7 characters and call them p1".
- The
-\end_layout
-
-\begin_layout LyX-Code
- second pattern unit is
-\end_layout
-
-\begin_layout LyX-Code
- 3...8
-\end_layout
-
-\begin_layout LyX-Code
- which means "then match 3 to 8 characters".
- The last pattern unit
-\end_layout
-
-\begin_layout LyX-Code
- is
-\end_layout
-
-\begin_layout LyX-Code
- ~p1
-\end_layout
-
-\begin_layout LyX-Code
- which means "match the reverse complement of p1".
- The first
-\end_layout
-
-\begin_layout LyX-Code
- reported hit is shown as
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[6,27]
-\end_layout
-
-\begin_layout LyX-Code
- cguaacc ggttaacc gguuacg
-\end_layout
-
-\begin_layout LyX-Code
- which states that characters 6 through 27 of sequence tst1 were
-\end_layout
-
-\begin_layout LyX-Code
- matched.
- "cguaac" matched the first pattern unit, "ggttaacc" the
-\end_layout
-
-\begin_layout LyX-Code
- second, and "gguuacg" the third.
- This is an example of a common
-\end_layout
-
-\begin_layout LyX-Code
- type of pattern used to search for sections of DNA or RNA that
-\end_layout
-
-\begin_layout LyX-Code
- would fold into a hairpin loop.
-\end_layout
-
-\begin_layout LyX-Code
-Searching Both Strands
-\end_layout
-
-\begin_layout LyX-Code
- Now for a short aside: scan_for_matches only searched the
-\end_layout
-
-\begin_layout LyX-Code
- sequences in the input file; it did not search the opposite
-\end_layout
-
-\begin_layout LyX-Code
- strand.
- With a pattern of the sort we just used, there is not
-\end_layout
-
-\begin_layout LyX-Code
- need o search the opposite strand.
- However, it is normally the
-\end_layout
-
-\begin_layout LyX-Code
- case that you will wish to search both the sequence and the
-\end_layout
-
-\begin_layout LyX-Code
- opposite strand (i.e., the reverse complement of the sequence).
-\end_layout
-
-\begin_layout LyX-Code
- To do that, you would just use the "-c" command line.
- For example,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches -c pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- Hits on the opposite strand will show a beginning location greater
-\end_layout
-
-\begin_layout LyX-Code
- than te end location of the match.
-\end_layout
-
-\begin_layout LyX-Code
-Defining Pairing Rules and Allowing Mismatches, Insertions, and Deletions
-\end_layout
-
-\begin_layout LyX-Code
- Let us stop now and ask "What additional features would one need to
-\end_layout
-
-\begin_layout LyX-Code
- really find the kinds of loop structures that characterize tRNAs,
-\end_layout
-
-\begin_layout LyX-Code
- rRNAs, and so forth?" I can immediately think of two:
-\end_layout
-
-\begin_layout LyX-Code
- a) you will need to be able to allow non-standard pairings
-\end_layout
-
-\begin_layout LyX-Code
- (those other than G-C and A-U), and
-\end_layout
-
-\begin_layout LyX-Code
- b) you will need to be able to tolerate some number of
-\end_layout
-
-\begin_layout LyX-Code
- mismatches and bulges.
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- Let me first show you how to handle non-standard "rules for
-\end_layout
-
-\begin_layout LyX-Code
- pairing in reverse complements".
- Consider the following pattern,
-\end_layout
-
-\begin_layout LyX-Code
- which I show as two line (you may use as many lines as you like in
-\end_layout
-
-\begin_layout LyX-Code
- forming a pattern, although you can only break a pattern at points
-\end_layout
-
-\begin_layout LyX-Code
- where space would be legal):
-\end_layout
-
-\begin_layout LyX-Code
- r1={au,ua,gc,cg,gu,ug,ga,ag}
-\end_layout
-
-\begin_layout LyX-Code
- p1=2...3 0...4 p2=2...5 1...5 r1~p2 0...4 ~p1
-\end_layout
-
-\begin_layout LyX-Code
- The first "pattern unit" does not actually match anything; rather,
-\end_layout
-
-\begin_layout LyX-Code
- it defines a "pairing rule" in which standard pairings are
-\end_layout
-
-\begin_layout LyX-Code
- allowed, as well as G-A and A-G (in case you wondered, Us and Ts
-\end_layout
-
-\begin_layout LyX-Code
- and upper and lower case can be used interchangably; for example
-\end_layout
-
-\begin_layout LyX-Code
- r1={AT,UA,gc,cg} could be used to define the "standard rule" for
-\end_layout
-
-\begin_layout LyX-Code
- pairings).
- The second line consists of six pattern units which
-\end_layout
-
-\begin_layout LyX-Code
- may be interpreted as follows:
-\end_layout
-
-\begin_layout LyX-Code
- p1=2...3 match 2 or 3 characters (call it p1)
-\end_layout
-
-\begin_layout LyX-Code
- 0...4 match 0 to 4 characters
-\end_layout
-
-\begin_layout LyX-Code
- p2=2...5 match 2 to 5 characters (call it p2)
-\end_layout
-
-\begin_layout LyX-Code
- 1...5 match 1 to 5 characters
-\end_layout
-
-\begin_layout LyX-Code
- r1~p2 match the reverse complement of p2,
-\end_layout
-
-\begin_layout LyX-Code
- allowing G-A and A-G pairs
-\end_layout
-
-\begin_layout LyX-Code
- 0...4 match 0 to 4 characters
-\end_layout
-
-\begin_layout LyX-Code
- ~p1 match the reverse complement of p1
-\end_layout
-
-\begin_layout LyX-Code
- allowing only G-C, C-G, A-T, and T-A pairs
-\end_layout
-
-\begin_layout LyX-Code
- Thus, r1~p2 means "match the reverse complement of p2 using rule r1".
-\end_layout
-
-\begin_layout LyX-Code
- Now let us consider the issue of tolerating mismatches and bulges.
-\end_layout
-
-\begin_layout LyX-Code
- You may add a "qualifier" to the pattern unit that gives the
-\end_layout
-
-\begin_layout LyX-Code
- tolerable number of "mismatches, deletions, and insertions".
-\end_layout
-
-\begin_layout LyX-Code
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- p1=10...10 3...8 ~p1[1,2,1]
-\end_layout
-
-\begin_layout LyX-Code
- means that the third pattern unit must match 10 characters,
-\end_layout
-
-\begin_layout LyX-Code
- allowing one "mismatch" (a pairing other than G-C, C-G, A-T, or
-\end_layout
-
-\begin_layout LyX-Code
- T-A), two deletions (a deletion is a character that occurs in p1,
-\end_layout
-
-\begin_layout LyX-Code
- but has been "deleted" from the string matched by ~p1), and one
-\end_layout
-
-\begin_layout LyX-Code
- insertion (an "insertion" is a character that occurs in the string
-\end_layout
-
-\begin_layout LyX-Code
- matched by ~p1, but not for which no corresponding character
-\end_layout
-
-\begin_layout LyX-Code
- occurs in p1).
- In this case, the pattern would match
-\end_layout
-
-\begin_layout LyX-Code
- ACGTACGTAC GGGGGGGG GCGTTACCT
-\end_layout
-
-\begin_layout LyX-Code
- which is, you must admit, a fairly weak loop.
- It is common to
-\end_layout
-
-\begin_layout LyX-Code
- allow mismatches, but you will find yourself using insertions and
-\end_layout
-
-\begin_layout LyX-Code
- deletions much more rarely.
- In any event, you should note that
-\end_layout
-
-\begin_layout LyX-Code
- allowing mismatches, insertions, and deletions does force the
-\end_layout
-
-\begin_layout LyX-Code
- program to try many additional possible pairings, so it does slow
-\end_layout
-
-\begin_layout LyX-Code
- things down a bit.
-\end_layout
-
-\begin_layout LyX-Code
-How Patterns Are Matched
-\end_layout
-
-\begin_layout LyX-Code
- Now is as good a time as any to discuss the basic flow of control
-\end_layout
-
-\begin_layout LyX-Code
- when matching patterns.
- Recall that a "pattern" is a sequence of
-\end_layout
-
-\begin_layout LyX-Code
- "pattern units".
- Suppose that the pattern units were
-\end_layout
-
-\begin_layout LyX-Code
- u1 u2 u3 u4 ...
- un
-\end_layout
-
-\begin_layout LyX-Code
- The scan of a sequence S begins by setting the current position
-\end_layout
-
-\begin_layout LyX-Code
- to 1.
- Then, an attempt is made to match u1 starting at the
-\end_layout
-
-\begin_layout LyX-Code
- current position.
- Each attempt to match a pattern unit can
-\end_layout
-
-\begin_layout LyX-Code
- succeed or fail.
- If it succeeds, then an attempt is made to match
-\end_layout
-
-\begin_layout LyX-Code
- the next unit.
- If it fails, then an attempt is made to find an
-\end_layout
-
-\begin_layout LyX-Code
- alternative match for the immediately preceding pattern unit.
- If
-\end_layout
-
-\begin_layout LyX-Code
- this succeeds, then we proceed forward again to the next unit.
- If
-\end_layout
-
-\begin_layout LyX-Code
- it fails we go back to the preceding unit.
- This process is called
-\end_layout
-
-\begin_layout LyX-Code
- "backtracking".
- If there are no previous units, then the current
-\end_layout
-
-\begin_layout LyX-Code
- position is incremented by one, and everything starts again.
- This
-\end_layout
-
-\begin_layout LyX-Code
- proceeds until either the current position goes past the end of
-\end_layout
-
-\begin_layout LyX-Code
- the sequence or all of the pattern units succeed.
- On success,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches reports the "hit", the current position is set
-\end_layout
-
-\begin_layout LyX-Code
- just past the hit, and an attempt is made to find another hit.
-\end_layout
-
-\begin_layout LyX-Code
- If you wish to limit the scan to simply finding a maximum of, say,
-\end_layout
-
-\begin_layout LyX-Code
- 10 hits, you can use the -n option (-n 10 would set the limit to
-\end_layout
-
-\begin_layout LyX-Code
- 10 reported hits).
- For example,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches -c -n 1 pat_file < test_dna_input
-\end_layout
-
-\begin_layout LyX-Code
- would search for just the first hit (and would stop searching the
-\end_layout
-
-\begin_layout LyX-Code
- current sequences or any that follow in the input file).
-\end_layout
-
-\begin_layout LyX-Code
-Searching for repeats:
-\end_layout
-
-\begin_layout LyX-Code
- In the last section, I discussed almost all of the details
-\end_layout
-
-\begin_layout LyX-Code
- required to allow you to look for repeats.
- Consider the following
-\end_layout
-
-\begin_layout LyX-Code
- set of patterns:
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...6 3...8 p1 (find exact 6 character repeat separated
-\end_layout
-
-\begin_layout LyX-Code
- by to 8 characters)
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...6 3..8 p1[1,0,0] (allow one mismatch)
-\end_layout
-
-\begin_layout LyX-Code
- p1=3...3 p1[1,0,0] p1[1,0,0] p1[1,0,0]
-\end_layout
-
-\begin_layout LyX-Code
- (match 12 characters that are the remains
-\end_layout
-
-\begin_layout LyX-Code
- of a 3-character sequence occurring 4 times)
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- p1=4...8 0...3 p2=6...8 p1 0...3 p2
-\end_layout
-
-\begin_layout LyX-Code
- (This would match things like
-\end_layout
-
-\begin_layout LyX-Code
- ATCT G TCTTT ATCT TG TCTTT
-\end_layout
-
-\begin_layout LyX-Code
- )
-\end_layout
-
-\begin_layout LyX-Code
-Searching for particular sequences:
-\end_layout
-
-\begin_layout LyX-Code
- Occasionally, one wishes to match a specific, known sequence.
-\end_layout
-
-\begin_layout LyX-Code
- In such a case, you can just give the sequence (along with an
-\end_layout
-
-\begin_layout LyX-Code
- optional statement of the allowable mismatches, insertions, and
-\end_layout
-
-\begin_layout LyX-Code
- deletions).
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...8 GAGA ~p1 (match a hairpin with GAGA as the loop)
-\end_layout
-
-\begin_layout LyX-Code
- RRRRYYYY (match 4 purines followed by 4 pyrimidines)
-\end_layout
-
-\begin_layout LyX-Code
- TATAA[1,0,0] (match TATAA, allowing 1 mismatch)
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-Matches against a "weight matrix":
-\end_layout
-
-\begin_layout LyX-Code
- I will conclude my examples of the types of pattern units
-\end_layout
-
-\begin_layout LyX-Code
- available for matching against nucleotide sequences by discussing a
-\end_layout
-
-\begin_layout LyX-Code
- crude implemetation of matching using a "weight matrix".
- While I
-\end_layout
-
-\begin_layout LyX-Code
- am less than overwhelmed with the syntax that I chose, I think that
-\end_layout
-
-\begin_layout LyX-Code
- the reader should be aware that I was thinking of generating
-\end_layout
-
-\begin_layout LyX-Code
- patterns containing such pattern units automatically from
-\end_layout
-
-\begin_layout LyX-Code
- alignments (and did not really plan on typing such things in by
-\end_layout
-
-\begin_layout LyX-Code
- hand very often).
- Anyway, suppose that you wanted to match a
-\end_layout
-
-\begin_layout LyX-Code
- sequence of eight characters.
- The "consensus" of these eight
-\end_layout
-
-\begin_layout LyX-Code
- characters is GRCACCGS, but the actual "frequencies of occurrence"
-\end_layout
-
-\begin_layout LyX-Code
- are given in the matrix below.
- Thus, the first character is an A
-\end_layout
-
-\begin_layout LyX-Code
- 16% the time and a G 84% of the time.
- The second is an A 57% of
-\end_layout
-
-\begin_layout LyX-Code
- the time, a C 10% of the time, a G 29% of the time, and a T 4% of
-\end_layout
-
-\begin_layout LyX-Code
- the time.
-
-\end_layout
-
-\begin_layout LyX-Code
- C1 C2 C3 C4 C5 C6 C7 C8
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- A 16 57 0 95 0 18 0 0
-\end_layout
-
-\begin_layout LyX-Code
- C 0 10 80 0 100 60 0 50
-\end_layout
-
-\begin_layout LyX-Code
- G 84 29 0 0 0 20 100 50
-\end_layout
-
-\begin_layout LyX-Code
- T 0 4 20 5 0 2 0 0
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- One could use the following pattern unit to search for inexact
-\end_layout
-
-\begin_layout LyX-Code
- matches related to such a "weight matrix":
-\end_layout
-
-\begin_layout LyX-Code
- {(16,0,84,0),(57,10,29,4),(0,80,0,20),(95,0,0,5),
-\end_layout
-
-\begin_layout LyX-Code
- (0,100,0,0),(18,60,20,2),(0,0,100,0),(0,50,50,0)} > 450
-\end_layout
-
-\begin_layout LyX-Code
- This pattern unit will attempt to match exactly eight characters.
-\end_layout
-
-\begin_layout LyX-Code
- For each character in the sequence, the entry in the corresponding
-\end_layout
-
-\begin_layout LyX-Code
- tuple is added to an accumulated sum.
- If the sum is greater than
-\end_layout
-
-\begin_layout LyX-Code
- 450, the match succeeds; else it fails.
-\end_layout
-
-\begin_layout LyX-Code
- Recently, this feature was upgraded to allow ranges.
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- 600 > {(16,0,84,0),(57,10,29,4),(0,80,0,20),(95,0,0,5),
-\end_layout
-
-\begin_layout LyX-Code
- (0,100,0,0),(18,60,20,2),(0,0,100,0),(0,50,50,0)} > 450
-\end_layout
-
-\begin_layout LyX-Code
- will work, as well.
-\end_layout
-
-\begin_layout LyX-Code
-Allowing Alternatives:
-\end_layout
-
-\begin_layout LyX-Code
- Very occasionally, you may wish to allow alternative pattern units
-\end_layout
-
-\begin_layout LyX-Code
- (i.e., "match either A or B").
- You can do this using something
-\end_layout
-
-\begin_layout LyX-Code
- like
-\end_layout
-
-\begin_layout LyX-Code
- ( GAGA | GCGCA)
-\end_layout
-
-\begin_layout LyX-Code
- which says "match either GAGA or GCGCA".
- You may take
-\end_layout
-
-\begin_layout LyX-Code
- alternatives of a list of pattern units, for example
-\end_layout
-
-\begin_layout LyX-Code
- (p1=3...3 3...8 ~p1 | p1=5...5 4...4 ~p1 GGG)
-\end_layout
-
-\begin_layout LyX-Code
- would match one of two sequences of pattern units.
- There is one
-\end_layout
-
-\begin_layout LyX-Code
- clumsy aspect of the syntax: to match a list of alternatives, you
-\end_layout
-
-\begin_layout LyX-Code
- need to fully the request.
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- (GAGA | (GCGCA | TTCGA))
-\end_layout
-
-\begin_layout LyX-Code
- would be needed to try the three alternatives.
-\end_layout
-
-\begin_layout LyX-Code
-One Minor Extension
-\end_layout
-
-\begin_layout LyX-Code
- Sometimes a pattern will contain a sequence of distinct ranges,
-\end_layout
-
-\begin_layout LyX-Code
- and you might wish to limit the sum of the lengths of the matched
-\end_layout
-
-\begin_layout LyX-Code
- subsequences.
- For example, suppose that you basically wanted to
-\end_layout
-
-\begin_layout LyX-Code
- match something like
-\end_layout
-
-\begin_layout LyX-Code
- ARRYYTT p1=0...5 GCA[1,0,0] p2=1...6 ~p1 4...8 ~p2 p3=4...10 CCT
-\end_layout
-
-\begin_layout LyX-Code
- but that the sum of the lengths of p1, p2, and p3 must not exceed
-\end_layout
-
-\begin_layout LyX-Code
- eight characters.
- To do this, you could add
-\end_layout
-
-\begin_layout LyX-Code
- length(p1+p2+p3) < 9
-\end_layout
-
-\begin_layout LyX-Code
- as the last pattern unit.
- It will just succeed or fail (but does
-\end_layout
-
-\begin_layout LyX-Code
- not actually match any characters in the sequence).
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-Matching Protein Sequences
-\end_layout
-
-\begin_layout LyX-Code
- Suppose that the input file contains protein sequences.
- In this
-\end_layout
-
-\begin_layout LyX-Code
- case, you must invoke scan_for_matches with the "-p" option.
- You
-\end_layout
-
-\begin_layout LyX-Code
- cannot use aspects of the language that relate directly to
-\end_layout
-
-\begin_layout LyX-Code
- nucleotide sequences (e.g., the -c command line option or pattern
-\end_layout
-
-\begin_layout LyX-Code
- constructs referring to the reverse complement of a previously
-\end_layout
-
-\begin_layout LyX-Code
- matched unit).
-
-\end_layout
-
-\begin_layout LyX-Code
- You also have two additional constructs that allow you to match
-\end_layout
-
-\begin_layout LyX-Code
- either "one of a set of amino acids" or "any amino acid other than
-\end_layout
-
-\begin_layout LyX-Code
- those a given set".
- For example,
-\end_layout
-
-\begin_layout LyX-Code
- p1=0...4 any(HQD) 1...3 notany(HK) p1
-\end_layout
-
-\begin_layout LyX-Code
- would successfully match a string like
-\end_layout
-
-\begin_layout LyX-Code
- YWV D AA C YWV
-\end_layout
-
-\begin_layout LyX-Code
-Using the show_hits Utility
-\end_layout
-
-\begin_layout LyX-Code
- When viewing a large set of complex matches, you might find it
-\end_layout
-
-\begin_layout LyX-Code
- convenient to post-process the scan_for_matches output to get a
-\end_layout
-
-\begin_layout LyX-Code
- more readable version.
- We provide a simple post-processor called
-\end_layout
-
-\begin_layout LyX-Code
- "show_hits".
- To see its effect, just pipe the output of a
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches into show_hits:
-\end_layout
-
-\begin_layout LyX-Code
- Normal Output:
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches -c pat_file < tmp
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[1,28]
-\end_layout
-
-\begin_layout LyX-Code
- gtacguaacc ggttaac cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- >tst1:[28,1]
-\end_layout
-
-\begin_layout LyX-Code
- gtacgtaacc ggttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- >tst2:[2,31]
-\end_layout
-
-\begin_layout LyX-Code
- CGTACGUAAC C GGTTAACC GGUUACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- >tst2:[31,2]
-\end_layout
-
-\begin_layout LyX-Code
- CGTACGTAAC C GGTTAACC GGTTACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- >tst3:[3,32]
-\end_layout
-
-\begin_layout LyX-Code
- gtacguaacc g gttaactt cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- >tst3:[32,3]
-\end_layout
-
-\begin_layout LyX-Code
- gtacgtaacc g aagttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- Piped Through show_hits:
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches -c pat_file < tmp | show_hits
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[1,28]: gtacguaacc ggttaac cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[28,1]: gtacgtaacc ggttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[2,31]: CGTACGUAAC C GGTTAACC GGUUACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[31,2]: CGTACGTAAC C GGTTAACC GGTTACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[3,32]: gtacguaacc g gttaactt cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[32,3]: gtacgtaacc g aagttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- clone%
-\end_layout
-
-\begin_layout LyX-Code
- Optionally, you can specify which of the "fields" in the matches
-\end_layout
-
-\begin_layout LyX-Code
- you wish to sort on, and show_hits will sort them.
- The field
-\end_layout
-
-\begin_layout LyX-Code
- numbers start with 0.
- So, you might get something like
-\end_layout
-
-\begin_layout LyX-Code
- clone% scan_for_matches -c pat_file < tmp | show_hits 2 1
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[2,31]: CGTACGUAAC C GGTTAACC GGUUACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst2:[31,2]: CGTACGTAAC C GGTTAACC GGTTACGTACG
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[32,3]: gtacgtaacc g aagttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[1,28]: gtacguaacc ggttaac cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst1:[28,1]: gtacgtaacc ggttaac cggttacgtac
-\end_layout
-
-\begin_layout LyX-Code
- tst3:[3,32]: gtacguaacc g gttaactt cgguuacgtac
-\end_layout
-
-\begin_layout LyX-Code
- clone%
-\end_layout
-
-\begin_layout LyX-Code
- In this case, the hits have been sorted on fields 2 and 1 (that is,
-\end_layout
-
-\begin_layout LyX-Code
- the third and second matched subfields).
-\end_layout
-
-\begin_layout LyX-Code
- show_hits is just one possible little post-processor, and you
-\end_layout
-
-\begin_layout LyX-Code
- might well wish to write a customized one for yourself.
-\end_layout
-
-\begin_layout LyX-Code
-Reducing the Cost of a Search
-\end_layout
-
-\begin_layout LyX-Code
- The scan_for_matches utility uses a fairly simple search, and may
-\end_layout
-
-\begin_layout LyX-Code
- consume large amounts of CPU time for complex patterns.
- Someday,
-\end_layout
-
-\begin_layout LyX-Code
- I may decide to optimize the code.
- However, until then, let me
-\end_layout
-
-\begin_layout LyX-Code
- mention one useful technique.
-
-\end_layout
-
-\begin_layout LyX-Code
- When you have a complex pattern that includes a number of varying
-\end_layout
-
-\begin_layout LyX-Code
- ranges, imprecise matches, and so forth, it is useful to
-\end_layout
-
-\begin_layout LyX-Code
- "pipeline" matches.
- That is, form a simpler pattern that can be
-\end_layout
-
-\begin_layout LyX-Code
- used to scan through a large database extracting sections that
-\end_layout
-
-\begin_layout LyX-Code
- might be matched by the more complex pattern.
- Let me illustrate
-\end_layout
-
-\begin_layout LyX-Code
- with a short example.
- Suppose that you really wished to match the
-\end_layout
-
-\begin_layout LyX-Code
- pattern
-\end_layout
-
-\begin_layout LyX-Code
- p1=3...5 0...8 ~p1[1,1,0] p2=6...7 3...6 AGC 3...5 RYGC ~p2[1,0,0]
-\end_layout
-
-\begin_layout LyX-Code
- In this case, the pattern units AGC 3...5 RYGC can be used to rapidly
-\end_layout
-
-\begin_layout LyX-Code
- constrain the overall search.
- You can preprocess the overall
-\end_layout
-
-\begin_layout LyX-Code
- database using the pattern:
-\end_layout
-
-\begin_layout LyX-Code
- 31...31 AGC 3...5 RYGC 7...7
-\end_layout
-
-\begin_layout LyX-Code
- Put the complex pattern in pat_file1 and the simpler pattern in
-\end_layout
-
-\begin_layout LyX-Code
- pat_file2.
- Then use,
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches -c pat_file2 < nucleotide_database |
-\end_layout
-
-\begin_layout LyX-Code
- scan_for_matches pat_file1
-\end_layout
-
-\begin_layout LyX-Code
- The output will show things like
-\end_layout
-
-\begin_layout LyX-Code
- >seqid:[232,280][2,47]
-\end_layout
-
-\begin_layout LyX-Code
- matches pieces
-\end_layout
-
-\begin_layout LyX-Code
- Then, the actual section of the sequence that was matched can be
-\end_layout
-
-\begin_layout LyX-Code
- easily computed as [233,278] (remember, the positions start from
-\end_layout
-
-\begin_layout LyX-Code
- 1, not 0).
-\end_layout
-
-\begin_layout LyX-Code
- Let me finally add, you should do a few short experiments to see
-\end_layout
-
-\begin_layout LyX-Code
- whether or not such pipelining actually improves performance -- it
-\end_layout
-
-\begin_layout LyX-Code
- is not always obvious where the time is going, and I have
-\end_layout
-
-\begin_layout LyX-Code
- sometimes found that the added complexity of pipelining actually
-\end_layout
-
-\begin_layout LyX-Code
- slowed things up.
- It gets its best improvements when there are
-\end_layout
-
-\begin_layout LyX-Code
- exact matches of more than just a few characters that can be
-\end_layout
-
-\begin_layout LyX-Code
- rapidly used to eliminate large sections of the database.
-\end_layout
-
-\begin_layout LyX-Code
-=============
-\end_layout
-
-\begin_layout LyX-Code
-Additions:
-\end_layout
-
-\begin_layout LyX-Code
-Feb 9, 1995: the pattern units ^ and $ now work as in normal regular
-\end_layout
-
-\begin_layout LyX-Code
- expressions.
- That is
-\end_layout
-
-\begin_layout LyX-Code
- TTF $
-\end_layout
-
-\begin_layout LyX-Code
- matches only TTF at the end of the string and
-\end_layout
-
-\begin_layout LyX-Code
- ^ TTF
-\end_layout
-
-\begin_layout LyX-Code
- matches only an initial TTF
-\end_layout
-
-\begin_layout LyX-Code
- The pattern unit
-\end_layout
-
-\begin_layout LyX-Code
- <p1
-\end_layout
-
-\begin_layout LyX-Code
- matches the reverse of the string named p1.
- That is,
-\end_layout
-
-\begin_layout LyX-Code
- if p1 matched GCAT, then <p1 would match TACG.
- Thus,
-\end_layout
-
-\begin_layout LyX-Code
- p1=6...6 <p1
-\end_layout
-
-\begin_layout LyX-Code
- matches a real palindrome (not the biologically common
-\end_layout
-
-\begin_layout LyX-Code
- meaning of "reverse complement")
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\end_body
-\end_document
+++ /dev/null
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-\usepackage[colorlinks=true, urlcolor=blue, linkcolor=black]{hyperref}
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-\usepackage{babel}
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-
-\begin{document}
-
-\title{Biotools Cookbook}
-
-
-\author{Martin Asser Hansen}
-
-
-\publishers{John Mattick Group\\
-Institute for Molecular Bioscience\\
-University of Queensland\\
-Australia\\
-E-mail: mail@maasha.dk}
-
-\maketitle
-\thispagestyle{empty}
-
-\newpage{}
-
-\tableofcontents{}
-
-\listoffigures
-
-
-\newpage{}
-
-
-\section{Introduction}
-
-Biotools is a selection of simple tools that can be linked together
-(piped as we shall call it) in a very flexible manner to perform both
-simple and complex tasks. The fundamental idea is that biotools work
-on a data stream that will only terminate at the end of an analysis
-and that this data stream can be passed through several different
-biotools, each performing one specific task. The advantage of this
-approach is that a user can perform simple and complex tasks without
-having to write advanced code. Moreover, since the data format used
-to pass data between biotools is text based, biotools can be written
-by different developers in their favorite programming language ---
-and still the biotools will be able to work together.
-
-In the most simple form bioools can be piped together on the command
-line like this (using the pipe character '|'):
-
-\begin{lyxcode}
-read\_data~|~calculate\_something~|~write\_result
-\end{lyxcode}
-However, a more comprehensive analysis could be composed:
-
-\begin{lyxcode}
-read\_data~|~select\_entries~|~convert\_entries~|~search\_database~~
-
-evaluate\_results~|~plot\_diagram~|~plot\_another\_diagram~|
-
-load\_to\_database
-\end{lyxcode}
-The data stream that is piped through the biotools consists of records
-of key/value pairs in the same way a hash does in order to keep as
-simple a structure as possible. An example record can be seen below:
-
-\begin{lyxcode}
-
-
-REC\_TYPE:~PATSCAN
-
-MATCH:~AGATCAAGTG
-
-S\_BEG:~7
-
-S\_END:~16
-
-ALIGN\_LEN:~9
-
-S\_ID:~piR-t6
-
-STRAND:~+
-
-PATTERN:~AGATCAAGTG
-
--{}-{}-
-\end{lyxcode}
-The '-\/-\/-' denotes the delimiter of the records, and each key
-is a word followed by a ':' and a white-space and then the value.
-By convention the biotools only uses upper case keys (a list of used
-keys can be seen in Appendix~\ref{sec:Keys}). Since the records
-basically are hash structures this mean that the order of the keys
-in the stream is unordered, and in the above example it is pure coincidence
-that HIT\_BEG is displayed before HIT\_END, however, when the order
-of the keys is importent, the biotools will automagically see to that.
-
-All of the biotools are able to read and write a data stream to and
-from file as long as the records are in the biotools format. This
-means that if you are undertaking a lengthy analysis where one of
-the steps is time consuming, you may save the stream after this step,
-and subsequently start one or more analysis from that last step%
-\footnote{It is a goal that the biotools at some point will be able to dump
-the data stream to file in case one of the tools fail critically.%
-}. If you are running a lengthy analysis it is highly recommended that
-you create a small test sample of the data and run that through the
-pipeline --- and once you are satisfied with the result proceed with
-the full data set (see~\ref{sub:How-to-select-a-few-records}).
-
-
-\section{The Data Stream}
-
-
-\subsection{How to read the data stream from file?\label{sub:How-to-read-stream}}
-
-You want to read a data stream that you previously have saved to file
-in biotools format. This can be done implicetly or explicitly. The
-implicit way uses the 'stdout' stream of the Unix terminal:
-
-\begin{lyxcode}
-cat~|~<biotool>
-\end{lyxcode}
-cat is the Unix command that reads a file and output the result to
-'stdout' --- which in this case is piped to any biotool represented
-by the <biotool>. It is also possible to read the data stream using
-'<' to direct the 'stdout' stream into the biotool like this:
-
-\begin{lyxcode}
-<biotool>~<~<file>
-\end{lyxcode}
-However, that will not work if you pipe more biotools together. Then
-it is much safer to read the stream from a file explicitly like this:
-
-\begin{lyxcode}
-<biotool>~-{}-stream\_in=<file>
-\end{lyxcode}
-Here the filename <file> is explicetly given to the biotool <biotool>
-with the switch -\/-stream\_in. This switch works with all biotools.
-It is also possible to read in data from multiple sources by repeating
-the explicit read step:
-
-\begin{lyxcode}
-<biotool>~-{}-stream\_in=<file1>~|~<biotool>~-{}-stream\_in=<file2>
-\end{lyxcode}
-
-\subsection{How to write the data stream to file?\label{sub:How-to-write-stream}}
-
-In order to save the output stream from a biotool to file, so you
-can read in the stream again at a later time, you can do one of two
-things:
-
-\begin{lyxcode}
-<biotool>~>~<file>
-\end{lyxcode}
-All, the biotools write the data stream to 'stdout' by default which
-can be written to a file by redirecting 'stdout' to file using '>'
-, however, if one of the biotools for writing other formats is used
-then the both the biotools records as well as the result output will
-go to 'stdout' in a mixture causing havock! To avoid this you must
-use the switch -\/-stream\_out that explictly tells the biotool to
-write the output stream to file:
-
-\begin{lyxcode}
-<biotool>~-{}-stream\_out=<file>
-\end{lyxcode}
-The -\/-stream\_out switch works with all biotools.
-
-
-\subsection{How to terminate the data stream?}
-
-The data stream is never stops unless the user want to save the stream
-or by supplying the -\/-no\_stream switch that will terminate the
-stream:
-
-\begin{lyxcode}
-<biotool>~-{}-no\_stream
-\end{lyxcode}
-The -\/-no\_stream switch only works with those biotools where it
-makes sense that the user might want to terminale the data stream,
-\emph{i.e}. after an analysis step where the user wants to output
-the result, but not the data stream.
-
-
-\subsection{How to write my results to file?\label{sub:How-to-write-result}}
-
-Saving the result of an analysis to file can be done implicitly or
-explicitly. The implicit way:
-
-\begin{lyxcode}
-<biotool>~-{}-no\_stream~>~<file>
-\end{lyxcode}
-If you use '>' to redirect 'stdout' to file then it is important to
-use the -\/-no\_stream switch to avoid writing a mix of biotools
-records and result to the same file causing havock. The safe way is
-to use the -\/-result\_out switch which explicetly tells the biotool
-to write the result to a given file:
-
-\begin{lyxcode}
-<biotool>~-{}-result\_out=<file>
-\end{lyxcode}
-Using the above method will not terminate the stream, so it is possible
-to pipe that into another biotool generating different results:
-
-\begin{lyxcode}
-<biotool1>~-{}-result\_out=<file1>~|~<biotool2>~-{}-result\_out=<file2>
-\end{lyxcode}
-And still the data stream will continue unless terminated with -\/-no\_stream:
-
-\begin{lyxcode}
-<biotool>~-{}-result\_out=<file>~-{}-no\_stream
-\end{lyxcode}
-Or written to file using implicitly or explicity \eqref{sub:How-to-write-result}.
-The explicit way:
-
-\begin{lyxcode}
-<biotool>~-{}-result\_out=<file1>~-{}-stream\_out=<file2>
-\end{lyxcode}
-
-\subsection{How to read data from multiple sources?}
-
-To read multiple data sources, with the same type or different type
-of data do:
-
-\begin{lyxcode}
-<biotool1>~-{}-data\_in=<file1>~|~<biotool2>~-{}-data\_in=<file2>
-\end{lyxcode}
-where type is the data type a specific biotool reads.
-
-
-\section{Reading input}
-
-
-\subsection{How to read biotools input?}
-
-See \eqref{sub:How-to-read-stream}.
-
-
-\subsection{How to read in data?}
-
-Data in different formats can be read with the appropriate biotool
-for that format. The biotools are typicalled named 'read\_<data type>'
-such as \textbf{read\_fasta}, \textbf{read\_bed}, \textbf{read\_tab},
-etc., and all behave in a similar manner. Data can be read by supplying
-the -\/-data\_in switch and a file name to the file containing the
-data:
-
-\begin{lyxcode}
-<biotool>~-{}-data\_in=<file>
-\end{lyxcode}
-It is also possible to read in a saved biotools stream (see \ref{sub:How-to-read-stream})
-as well as reading data in one go:
-
-\begin{lyxcode}
-<biotool>~-{}-stream\_in=<file1>~-{}-data\_in=<file2>
-\end{lyxcode}
-If you want to read data from several files you can do this:
-
-\begin{lyxcode}
-<biotool>~-{}-data\_in=<file1>~|~<biotool>~-{}-data\_in=<file2>
-\end{lyxcode}
-If you have several data files you can read in all explicitly with
-a comma separated list:
-
-\begin{lyxcode}
-<biotool>~-{}-data\_in=file1,file2,file3
-\end{lyxcode}
-And it is also possible to use file globbing:
-
-\begin{lyxcode}
-<biotool>~-{}-data\_in={*}.fna
-\end{lyxcode}
-Or in a combination:
-
-\begin{lyxcode}
-<biotool>~-{}-data\_in=file1,/dir/{*}.fna
-\end{lyxcode}
-Finally, it is possible to read in data in different formats using
-the appropriate biotool for each format:
-
-\begin{lyxcode}
-<biotool1>~-{}-data\_in=<file1>~|~<biotool2>~-{}-data\_in=<file2>~...
-\end{lyxcode}
-
-\subsection{How to read FASTA input?}
-
-Sequences in FASTA format can be read explicitly using \textbf{read\_fasta}:
-
-\begin{lyxcode}
-read\_fasta~-{}-data\_in=<file>
-\end{lyxcode}
-
-\subsection{How to read alignment input?}
-
-If your alignment if FASTA formatted then you can \textbf{read\_align}.
-It is also possible to use \textbf{read\_fasta} since the data is
-FASTA formatted, however, with \textbf{read\_fasta} the key ALIGN
-will be omitted. The ALIGN key is used to determine which sequences
-belong to what alignment which is required for \textbf{write\_align}.
-
-\begin{lyxcode}
-read\_align~-{}-data\_in=<file>
-\end{lyxcode}
-
-\subsection{How to read tabular input?\label{sub:How-to-read-table}}
-
-Tabular input can be read with \textbf{read\_tab} which will read
-in all rows and chosen columns (separated by a given delimter) from
-a table in text format.
-
-The table below:
-
-\noindent \begin{center}
-\begin{tabular}{lll}
-Human & ATACGTCAG & 23524\tabularnewline
-Dog & AGCATGAC & 2442\tabularnewline
-Mouse & GACTG & 234\tabularnewline
-Cat & AAATGCA & 2342\tabularnewline
-\end{tabular}
-\par\end{center}
-
-Can be read using the command:
-
-\begin{lyxcode}
-read\_tab~-{}-data\_in=<file>
-\end{lyxcode}
-Which will result in four records, one for each row, where the keys
-V0, V1, V2 are the default keys for the organism, sequence, and count,
-respectively. It is possible to select a subset of colums to read
-by using the -\/-cols switch which takes a comma separated list of
-columns numbers (first column is designated 0) as argument. So to
-read in only the sequence and the count so that the count comes before
-the sequence do:
-
-\begin{lyxcode}
-read\_tab~-{}-data\_in=<file>~-{}-cols=2,1
-\end{lyxcode}
-It is also possible to name the columns with the -\/-keys switch:
-
-\begin{lyxcode}
-read\_tab~-{}-data\_in=<file>~-{}-cols=2,1~-{}-keys=COUNT,SEQ
-\end{lyxcode}
-
-\subsection{How to read BED input?}
-
-The BED (Browser Extensible Data%
-\footnote{\url{http://genome.ucsc.edu/FAQ/FAQformat}%
-}) format is a tabular format for data pertaining to one of the Eukaryotic
-genomes in the UCSC genome brower%
-\footnote{\url{http://genome.ucsc.edu/}%
-}. The BED format consists of up to 12 columns, where the first three
-are mandatory CHR, CHR\_BEG, and CHR\_END. The mandatory columns and
-any of the optional columns can all be read in easily with the \textbf{read\_bed}
-biotool.
-
-\begin{lyxcode}
-read\_bed~-{}-data\_in=<file>
-\end{lyxcode}
-It is also possible to read the BED file with \textbf{read\_tab} (see~\ref{sub:How-to-read-table}),
-however, that will be more cumbersome because you need to specify
-the keys:
-
-\begin{lyxcode}
-read\_tab~-{}-data\_in=<file>~-{}-keys=CHR,CHR\_BEG,CHR\_END~...
-\end{lyxcode}
-
-\subsection{How to read PSL input?}
-
-The PSL format is the output from BLAT and contains 21 mandatory fields
-that can be read with \textbf{read\_psl}:
-
-\begin{lyxcode}
-read\_psl~-{}-data\_in=<file>
-\end{lyxcode}
-
-\section{Writing output}
-
-All result output can be written explicitly to file using the -\/-result\_out
-switch which all result generating biotools have. It is also possible
-to write the result to file implicetly by directing 'stdout' to file
-using '>', however, that requires the -\/-no\_stream swich to prevent
-a mixture of data stream and results in the file. The explicit (and
-safe) way:
-
-\begin{lyxcode}
-...~|~<biotool>~-{}-result\_out=<file>
-\end{lyxcode}
-The implicit way:
-
-\begin{lyxcode}
-...~|~<biotool>~-{}-no\_stream~>~<file>
-\end{lyxcode}
-
-\subsection{How to write biotools output?}
-
-See \eqref{sub:How-to-write-stream}.
-
-
-\subsection{How to write FASTA output?\label{sub:How-to-write-fasta}}
-
-FASTA output can be written with \textbf{write\_fasta}.
-
-\begin{lyxcode}
-...~|~write\_fasta~-{}-result\_out=<file>
-\end{lyxcode}
-It is also possible to wrap the sequences to a given width using the
--\/-wrap switch allthough wrapping of sequence is generally an evil
-thing:
-
-\begin{lyxcode}
-...~|~write\_fasta~-{}-no\_stream~-{}-wrap=80
-\end{lyxcode}
-
-\subsection{How to write alignment output?\label{sub:How-to-write-alignment}}
-
-Pretty alignments with ruler%
-\footnote{'.' for every 10 residues, ':' for every 50, and '|' for every 100%
-} and consensus sequence can be created with \textbf{write\_align},
-what also have the optional -\/-wrap switch to break the alignment
-into blocks of a given width:
-
-\begin{lyxcode}
-...~|~write\_align~-{}-result\_out=<file>~-{}-wrap=80
-\end{lyxcode}
-If the number of sequnces in the alignment is 2 then a pairwise alignment
-will be output otherwise a multiple alignment. And if the sequence
-type, determined automagically, is protein, then residues and symbols
-(+,~:,~.) will be used to show consensus according to the Blosum62
-matrix.
-
-
-\subsection{How to write tabular output?\label{sub:How-to-write-tab}}
-
-Outputting the data stream as a table can be done with \textbf{write\_tab},
-which will write generate one row per record with the values as columns.
-If you supply the optional -\/-comment switch, when the first row
-in the table will be a 'comment' line prefixed with a '\#':
-
-\begin{lyxcode}
-...~|~write\_tab~-{}-result\_out=<file>~-{}-comment
-\end{lyxcode}
-You can also change the delimiter from the default (tab) to \emph{e.g.}
-',':
-
-\begin{lyxcode}
-...~|~write\_tab~-{}-result\_out=<file>~-{}-delimit=','
-\end{lyxcode}
-If you want the values output in a specific order you have to supply
-a comma separated list using the -\/-keys switch that will print
-only those keys in that order:
-
-\begin{lyxcode}
-...~|~write\_tab~-{}-result\_out=<file>~-{}-keys=SEQ\_NAME,COUNT
-\end{lyxcode}
-Alternatively, if you have some keys that you don't want in the tabular
-output, use the -\/-no\_keys switch. So to print all keys except
-SEQ and SEQ\_TYPE do:
-
-\begin{lyxcode}
-...~|~write\_tab~-{}-result\_out=<file>~-{}-no\_keys=SEQ,SEQ\_TYPE
-\end{lyxcode}
-Finally, if you have a stream containing a mix of different records
-types, \emph{e.g.} records with sequences and records with matches,
-then you can use \textbf{write\_tab} to output all the records in
-tabluar format, however, the -\/-comment, -\/-keys, and -\/-no\_keys
-switches will only respond to records of the first type encountered.
-The reason is that outputting mixed records is probably not what you
-want anyway, and you should remove all the unwanted records from the
-stream before outputting the table: \textbf{grab} is your friend (see~\ref{sub:How-to-grab}).
-
-
-\subsection{How to write a BED output?\label{sub:How-to-write-BED}}
-
-Data in BED format can be output if the records contain the mandatory
-keys CHR, CHR\_BEG, and CHR\_END using \textbf{write\_bed}. If the
-optional keys are also present, they will be output as well:
-
-\begin{lyxcode}
-write\_bed~-{}-result\_out=<file>
-\end{lyxcode}
-
-\subsection{How to write PSL output?\label{sub:How-to-write-PSL}}
-
-Data in PSL format can be output using \textbf{write\_psl:}
-
-\begin{lyxcode}
-write\_psl~-{}-result\_out=<file>
-\end{lyxcode}
-
-\section{Manipulating Records}
-
-
-\subsection{How to select a few records?\label{sub:How-to-select-a-few-records}}
-
-To quickly get an overview of your data you can limit the data stream
-to show a few records. This also very useful to test the pipeline
-with a few records if you are setting up a complex analysis using
-several biotools. That way you can inspect that all goes well before
-analyzing and waiting for the full data set. All of the read\_<type>
-biotools have the -\/-num switch which will take a number as argument
-and only that number of records will be read. So to read in the first
-10 FASTA entries from a file:
-
-\begin{lyxcode}
-read\_fasta~-{}-data\_in=test.fna~-{}-num=10
-\end{lyxcode}
-Another way of doing this is to use \textbf{head\_records} will limit
-the stream to show the first 10 records (default):
-
-\begin{lyxcode}
-...~|~head\_records
-\end{lyxcode}
-Using \textbf{head\_records} directly after one of the read\_<type>
-biotools will be a lot slower than using the -\/-num switch with
-the read\_<type> biotools, however, \textbf{head\_records} can also
-be used to limit the output from all the other biotools. It is also
-possible to give \textbf{head\_records} a number of records to show
-using the -\/-num switch. So to display the first 100 records do:
-
-\begin{lyxcode}
-...~|~head\_records~-{}-num=100
-\end{lyxcode}
-
-\subsection{How to count all records in the data stream?}
-
-To count all the records in the data stream use \textbf{count\_records},
-which adds one record (which is not included in the count) to the
-data stream. So to count the number of sequences in a FASTA file you
-can do this:
-
-\begin{lyxcode}
-cat~test.fna~|~read\_fasta~|~count\_records~-{}-no\_stream
-\end{lyxcode}
-Which will write the last record containing the count to 'stdout':
-
-\begin{lyxcode}
--{}-{}-
-
-count\_records:~630
-\end{lyxcode}
-It is also possible to write the count to file using the -\/-result\_out
-switch.
-
-
-\subsection{How to grab specific records?\label{sub:How-to-grab}}
-
-The biotool \textbf{grab} is related to the Unix grep and locates
-records based on matching keys and/or values using either a pattern,
-a Perl regex, or a numerical evaluation. To easily \textbf{grab} all
-records in the stream that has any mentioning of the pattern 'human'
-just pipe the data stream through \textbf{grab} like this:
-
-\begin{lyxcode}
-...~|~grab~-{}-pattern=human
-\end{lyxcode}
-This will search for the pattern 'human' in all keys and all values.
-The -\/-pattern switch takes a comma separated list of patterns,
-so in order to match multiple patterns do:
-
-\begin{lyxcode}
-...~|~grab~-{}-pattern=human,mouse
-\end{lyxcode}
-It is also possible to use the -\/-pattern\_in switch instead of
--\/-pattern. -\/-pattern\_in is used to read a file with one pattern
-per line:
-
-\begin{lyxcode}
-...~|~grab~-{}-pattern\_in=patterns.txt
-\end{lyxcode}
-If you want the opposite result --- to find all records that does
-not match the patterns, add the -\/-invert switch, which not only
-works with the -\/-pattern switch, but also with -\/-regex and -\/-eval:
-
-\begin{lyxcode}
-...~|~grab~-{}-pattern=human~-{}-invert
-\end{lyxcode}
-If you want to search the record keys only, \emph{e.g.} to find all
-records containing the key SEQ you can add the -\/-keys\_only switch.
-This will prevent matching of SEQ in any record value, and in fact
-SEQ is a not uncommon peptide sequence you could get an unwanted record.
-Also, this will give an increase in speed since only the keys are
-searched:
-
-\begin{lyxcode}
-...~|~grab~-{}-pattern=SEQ~-{}-keys\_only
-\end{lyxcode}
-However, if you are interested in finding the peptide sequence SEQ
-and not the SEQ key, just add the -\/-vals\_only switch instead:
-
-\begin{lyxcode}
-...~|~grab~-{}-pattern=SEQ~-{}-vals\_only
-\end{lyxcode}
-Also, if you want to grab for certain key/value pairs you can supply
-a comma separated list of keys whos values will then be searched using
-the -\/-keys switch. This is handy if your records contain large
-genomic sequences and you dont want to search the entire sequence
-for \emph{e.g.} the organism name --- it is much faster to tell \textbf{grab}
-which keys to search the value for:
-
-\begin{lyxcode}
-...~|~grab~-{}-pattern=human~-{}-keys=SEQ\_NAME
-
-
-\end{lyxcode}
-It is also possible to invoke flexible matching using regex (regular
-expressions) instead of simple pattern matching. In \textbf{grab}
-the regex engine is Perl based and allows use of different type of
-wild cards, alternatives, \emph{etc}%
-\footnote{\url{http://perldoc.perl.org/perlreref.html}%
-}. If you want to \textbf{grab} records withs the sequence ATCG or
-GCTA you can do this:
-
-\begin{lyxcode}
-...~|~grab~-{}-regex='ATCG|GCTA'
-\end{lyxcode}
-Or if you want to find sequences beginning with ATCG:
-
-\begin{lyxcode}
-...~|~grab~-{}-regex='\textasciicircum{}ATCG'
-\end{lyxcode}
-You can also use \textbf{grab} to locate records that fulfill a numerical
-property using the -\/-eval switch witch takes an expression in three
-parts. The first part is the key that holds the number we want to
-evaluate, the second part holds one the six operators:
-
-\begin{enumerate}
-\item Greater than: >
-\item Greater than or equal to: >=
-\item Less than: <
-\item Less than or equal to: <=
-\item Equal to: =
-\item Not equal to: !=
-\end{enumerate}
-And finally comes the number used in the evaluation. So to \textbf{grab}
-all records with a sequence length greater than 30:
-
-\begin{lyxcode}
-...~length\_seq~|~grab~-{}-eval='SEQ\_LEN~>~30'
-\end{lyxcode}
-If you want to locate all records containing the pattern 'human' and
-where the sequence length is greater that 30, you do this by running
-the stream through \textbf{grab} twice:
-
-\begin{lyxcode}
-...~|~grab~-{}-pattern='human'~|~length\_seq~|~grab~-{}-eval='SEQ\_LEN~>~30'
-\end{lyxcode}
-To get the best speed performance, use the most restrictive \textbf{grab}
-first.
-
-
-\subsection{How to remove keys from records?}
-
-To remove one or more specific keys from all records in the data stream
-use \textbf{remove\_keys} like this:
-
-\begin{lyxcode}
-...~|~remove\_keys~-{}-keys=SEQ,SEQ\_NAME
-\end{lyxcode}
-In the above example SEQ and SEQ\_NAME will be removed from all records
-if they exists in these. If all keys are removed from a record, then
-the record will be removed.
-
-
-\subsection{How to rename keys in records?}
-
-Sometimes you want to rename a record key, \emph{e.g.} if you have
-read in a two column table with sequence name and sequence in each
-column (see \ref{sub:How-to-read-table}) without specifying the key
-names, then the sequence name will be called V0 and the sequence V1
-as default in the \textbf{read\_tab} biotool. To rename the V0 and
-V1 keys we need to run the stream through \textbf{rename\_keys} twice
-(one for each key to rename):
-
-\begin{lyxcode}
-...~|~rename\_keys~-{}-keys=V0,SEQ\_NAME~|~rename\_keys~-{}-keys=V1,SEQ
-\end{lyxcode}
-The first instance of \textbf{rename\_keys} replaces all the V0 keys
-with SEQ\_NAME, and the second instance of \textbf{rename\_keys} replaces
-all the V1 keys with SEQ. \emph{Et viola} the data can now be used
-in the biotools that requires these keys.
-
-
-\section{Manipulating Sequences}
-
-
-\subsection{How to get sequence lengths?}
-
-The length for sequences in records can be determined with \textbf{length\_seq},
-which adds the key SEQ\_LEN to each record with the sequence length
-as the value. It also generates an extra record that is emitted last
-with the key TOTAL\_SEQ\_LEN showing the total length of all the sequences.
-
-\begin{lyxcode}
-read\_fasta~-{}-data\_in=<file>~|~length\_seq
-\end{lyxcode}
-It is also possible to determine the sequence length using the generic
-tool \textbf{length\_vals} (see \#\#\#), which determines the length
-of the values for a given list of keys:
-
-\begin{lyxcode}
-read\_fasta~-{}-data\_in=<file>~|~length\_vals~-{}-keys=SEQ
-\end{lyxcode}
-To obtain the total length of all sequences use \textbf{sum\_vals}
-like this:
-
-\begin{lyxcode}
-read\_fasta~-{}-data\_in=<file>~|~length\_vals~-{}-keys=SEQ
-
-|~sum\_vals~-{}-keys=SEQ\_LEN
-\end{lyxcode}
-The biotool \textbf{analyze\_seq} will also determine the length of
-each sequence (see~\ref{sub:How-to-analyze}).
-
-
-\subsection{How to analyze sequence composition?\label{sub:How-to-analyze}}
-
-If you want to find out the sequence type, composition, length, as
-well as GC content, indel content and proportions of soft and hard
-masked sequence, then use \textbf{analyze\_seq}. This handy biotool
-will determine all these things per sequence from which it is easy
-to get an overview using the \textbf{write\_tab} biotool to output
-a table (see~\ref{sub:How-to-write-tab}). So in order to determine
-the sequence composition of a FASTA file with just one entry containing
-the sequence 'ATCG' we just read the data with \textbf{read\_fasta}
-and run the output through \textbf{analyze\_seq} which will add the
-analysis to the record like this:
-
-\begin{lyxcode}
-read\_fasta~-{}-data\_in=test.fna~|~analyze\_seq~...
-
-
-
--{}-{}-
-
-GC\%:~50.00
-
-HARD\_MASK\%:~0.00
-
-RES:-:~0
-
-RES:.:~0
-
-RES:A:~1
-
-RES:B:~0
-
-RES:C:~1
-
-RES:D:~0
-
-RES:G:~1
-
-RES:H:~0
-
-RES:K:~0
-
-RES:M:~0
-
-RES:N:~0
-
-RES:R:~0
-
-RES:S:~0
-
-RES:T:~1
-
-RES:U:~0
-
-RES:V:~0
-
-RES:W:~0
-
-RES:Y:~0
-
-RES:\textasciitilde{}:~0
-
-SEQ:~ATCG
-
-SEQ\_LEN:~4
-
-SEQ\_NAME:~test
-
-SEQ\_TYPE:~DNA
-
-SOFT\_MASK\%:~0.00
-\end{lyxcode}
-Now to make a table of how may As, Ts, Cs, and Gs you can add the
-following:
-
-\begin{lyxcode}
-...~|~analyze\_seq~|~write\_tab~-{}-keys=RES:A,RES:T,RES:C,RES:G
-\end{lyxcode}
-Or if you want to see the proportions of hard and soft masked sequence:
-
-\begin{lyxcode}
-...~|~analyse\_seq~|~write\_tab~-{}-keys=HARD\_MASK\%,SOFT\_MASK\%
-\end{lyxcode}
-If you have a stack of sequences in one file and you want to determine
-the mean GC content you can do it using the \textbf{mean\_vals} biotool:
-
-\begin{lyxcode}
-read\_fasta~-{}-data\_in=test.fna~|~analyze\_seq~|~mean\_vals~-{}-keys=GC\%
-\end{lyxcode}
-Or if you want the total count of Ns you can use \textbf{sum\_vals}
-like this:
-
-\begin{lyxcode}
-read\_fasta~-{}-data\_in=test.fna~|~analyze\_seq~|~sum\_vals~-{}-keys=RES:N
-\end{lyxcode}
-
-\subsection{How to extract subsequences?\label{sub:How-to-extract}}
-
-In order to extract a subsequence from a longer sequence use the biotool
-extract\_seq, which will replace the sequence in the record with the
-subsequence (this behaviour should probably be modified to be dependant
-of a -\/-replace or a -\/-no\_replace switch). So to extract the
-first 20 residues from all sequences do (first residue is designated
-1):
-
-\begin{lyxcode}
-...~|~extract\_seq~-{}-beg=1~-{}-len=20
-\end{lyxcode}
-You can also specify a begin and end coordinate set:
-
-\begin{lyxcode}
-...~|~extract\_seq~-{}-beg=20~-{}-end=40
-\end{lyxcode}
-If you want the subsequences from position 20 to the sequence end
-do:
-
-\begin{lyxcode}
-...~|~extract\_seq~-{}-beg=20
-\end{lyxcode}
-If you want to extract subsequences a given distance from the sequence
-end you can do this by reversing the sequence with the biotool \textbf{reverse\_seq}
-\eqref{sub:How-to-reverse-seq}, followed by \textbf{extract\_seq}
-to get the subsequence, and then \textbf{reverse\_seq} again to get
-the subsequence back in the original orientation:
-
-\begin{lyxcode}
-read\_fasta~-{}-data\_in=test.fna~|~reverse\_seq
-
-|~extract\_seq~-{}-beg=10~-{}-len=10~|~reverse\_seq
-\end{lyxcode}
-
-\subsection{How to get genomic sequence?\label{sub:How-to-get-genomic-sequence}}
-
-The biotool \textbf{get\_genomic\_seq} can extract subsequences for
-a given genome specified with the -\/-genome switch explicitly using
-the -\/-beg and -\/-end/-\/-len switches:
-
-\begin{lyxcode}
-get\_genome\_seq~-{}-genome=<genome>~-{}-beg=1~-{}-len=100
-\end{lyxcode}
-Alternatively, \textbf{get\_genome\_seq} can be used to append the
-corresponding sequence to BED, PSL, and BLAST records:
-
-\begin{lyxcode}
-read\_bed~-{}-data\_in=<BED~file>~|~get\_genome\_seq~-{}-genome=<genome>
-\end{lyxcode}
-
-\subsection{How to upper-case sequences?}
-
-Sequences can be shifted from lower case to upper case using \textbf{uppercase\_seq}:
-
-\begin{lyxcode}
-...~|~uppercase\_seq
-\end{lyxcode}
-
-\subsection{How to reverse sequences?\label{sub:How-to-reverse-seq}}
-
-The order of residues in a sequence can be reversed using reverse\_seq:
-
-\begin{lyxcode}
-...~|~reverse\_seq
-\end{lyxcode}
-Note that in order to reverse/complement a sequence you also need
-the \textbf{complement\_seq} biotool (see~\ref{sub:How-to-complement}).
-
-
-\subsection{How to complement sequences?\label{sub:How-to-complement}}
-
-DNA and RNA sequences can be complemented with \textbf{complement\_seq},
-which automagically determines the sequence type:
-
-\begin{lyxcode}
-...~|~complement\_seq
-\end{lyxcode}
-Note that in order to reverse/complement a sequence you also need
-the \textbf{reverse\_seq} biotool (see~\ref{sub:How-to-reverse-seq}).
-
-
-\subsection{How to remove indels from sequnces?}
-
-Indels can be removed from sequences with the \textbf{remove\_indels}
-biotool. This is useful if you have aligned some sequences (see~\ref{sub:How-to-align})
-and extracted (see~\ref{sub:How-to-extract}) a block of subsequences
-from the alignment and you want to use these sequence in a search
-where you need to remove the indels first. '-', '\textasciitilde{}',
-and '.' are considered indels:
-
-\begin{lyxcode}
-...~|~remove\_indels
-\end{lyxcode}
-
-\subsection{How to split sequences into overlapping subsequences?}
-
-Sequences can be slit into overlapping subsequences with the \textbf{split\_seq}
-biotool.
-
-\begin{lyxcode}
-...~|~split\_seq~-{}-word\_size=20~-{}-uniq
-\end{lyxcode}
-
-\subsection{How to determine the oligo frequency?}
-
-In order to determine if any oligo usage is over represented in one
-or more sequences you can determine the frequency of oligos of a given
-size with \textbf{oligo\_freq}:
-
-\begin{lyxcode}
-...~|~oligo\_freq~-{}-word\_size=4
-\end{lyxcode}
-And if you have more than one sequence and want to accumulate the
-frequences you need the -\/-all switch:
-
-\begin{lyxcode}
-...~|~oligo\_freq~-{}-word\_size=4~-{}-all
-\end{lyxcode}
-To get a meaningful result you need to write the resulting frequencies
-as a table with \textbf{write\_tab} (see~\ref{sub:How-to-write-tab}),
-but first it is important to \textbf{grab} (see~\ref{sub:How-to-grab})
-the records with the frequencies to avoid full length sequences in
-the table:
-
-\begin{lyxcode}
-...~|~oligo\_freq~-{}-word\_size=4~-{}-all~|~grab~-{}-pattern=OLIGO~-{}-keys\_only
-
-|~write\_tab~-{}-no\_stream
-\end{lyxcode}
-And the resulting frequency table can be sorted with Unix sort (man
-sort).
-
-
-\subsection{How to search for sequences in genomes?}
-
-See the following biotool:
-
-\begin{itemize}
-\item \textbf{patscan\_seq} \eqref{sub:How-to-use-patscan}
-\item \textbf{blat\_seq} \eqref{sub:How-to-use-BLAT}
-\item \textbf{blast\_seq} \eqref{sub:How-to-use-BLAST}
-\item \textbf{vmatch\_seq} \eqref{sub:How-to-use-Vmatch}
-\end{itemize}
-
-\subsection{How to search sequences for a pattern?\label{sub:How-to-use-patscan}}
-
-It is possible to search sequences in the data stream for patterns
-using the \textbf{patscan\_seq} biotool which utilizes the powerful
-scan\_for\_matches engine. Consult the documentation for scan\_for\_matches
-in order to learn how to define patterns (the documentation is included
-in Appendix~\ref{sec:scan_for_matches-README}).
-
-To search all sequences for a simple pattern consisting of the sequence
-ATCGATCG allowing for 3 mismatches, 2 insertions and 1 deletion:
-
-\begin{lyxcode}
-read\_fasta~-{}-data\_in=<file>~|~patscan\_seq~-{}-pattern='ATCGATCG{[}3,2,1]'
-\end{lyxcode}
-The -\/-pattern switch takes a comma seperated list of patterns,
-so if you want to search for more that one pattern do:
-
-\begin{lyxcode}
-...~|~patscan\_seq~-{}-pattern='ATCGATCG{[}3,2,1],GCTAGCTA{[}3,2,1]'
-\end{lyxcode}
-It is also possible to have a list of different patterns to search
-for in a file with one pattern per line. In order to get \textbf{patscan\_seq}
-to read these patterns use the -\/-pattern\_in switch:
-
-\begin{lyxcode}
-...~|~patscan\_seq~-{}-pattern\_in=<file>
-\end{lyxcode}
-To also scan the complementary strand in nucleotide sequences (\textbf{patscan\_seq}
-automagically determines the sequence type) you need to add the -\/-comp
-switch:
-
-\begin{lyxcode}
-...~|~patscan\_seq~-{}-pattern=<pattern>~-{}-comp
-\end{lyxcode}
-It is also possible to use \textbf{patscan\_seq} to output those records
-that does not contain a certain pattern by using the -\/-invert switch:
-
-\begin{lyxcode}
-...~|~patscan\_seq~-{}-pattern=<pattern>~-{}-invert
-\end{lyxcode}
-Finally, \textbf{patscan\_seq} can also scan for patterns in a given
-genome sequence, instead of sequences in the stream, using the -\/-genome
-switch:
-
-\begin{lyxcode}
-patscan~-{}-pattern=<pattern>~-{}-genome=<genome>
-\end{lyxcode}
-
-\subsection{How to use BLAT for sequence search?\label{sub:How-to-use-BLAT}}
-
-Sequences in the data stream can be matched against supported genomes
-using \textbf{blat\_seq} which is a biotool using BLAT as the name
-might suggest. Currently only Mouse and Human genomes are available
-and it is not possible to use OOC files since there is still a need
-for a local repository for genome files. Otherwise it is just:
-
-\begin{lyxcode}
-read\_fasta~-{}-data\_in=<file>~|~blat\_seq~-{}-genome=<genome>
-\end{lyxcode}
-The search results can then be written to file with \textbf{write\_psl}
-(see~\ref{sub:How-to-write-PSL}) or \textbf{write\_bed} (see~\ref{sub:How-to-write-BED})
-allthough with \textbf{write\_bed} some information will be lost).
-It is also possible to plot chromosome distribution of the search
-results using \textbf{plot\_chrdist} (see~\ref{sub:How-to-plot-chrdist})
-or the distribution of the match lengths using \textbf{plot\_lendist}
-(see~\ref{sub:How-to-plot-lendist}) or a karyogram with the hits
-using \textbf{plot\_karyogram} (see~\ref{sub:How-to-plot-karyogram}).
-
-
-\subsection{How to use BLAST for sequence search?\label{sub:How-to-use-BLAST}}
-
-Two biotools exist for blasting sequences: \textbf{create\_blast\_db}
-is used to create the BLAST database required for BLAST which is queried
-using the biotool \textbf{blast\_seq}. So in order to create a BLAST
-database from sequences in the data stream you simple run:
-
-\begin{lyxcode}
-...~|~create\_blast\_db~-{}-database=my\_database~-{}-no\_stream
-\end{lyxcode}
-The type of sequence to use for the database is automagically determined
-by \textbf{create\_blast\_db}, but don't have a mixture of peptide
-and nucleic acids sequences in the stream. The -\/-database switch
-takes a path as argument, but will default to 'blastdb\_<time\_stamp>
-if not set.
-
-The resulting database can now be queried with sequences in another
-data stream using \textbf{blast\_seq}:
-
-\begin{lyxcode}
-...~|~blast\_seq~-{}-database=my\_database
-\end{lyxcode}
-Again, the sequence type is determined automagically and the appropriate
-BLAST program is guessed (see below table), however, the program name
-can be overruled with the -\/-program switch.
-
-\noindent \begin{center}
-\begin{tabular}{ccc}
-Subject sequence & Query sequence & Program guess\tabularnewline
-\hline
-Nucleotide & Nucleotide & blastn\tabularnewline
-Protein & Protein & blastp\tabularnewline
-Protein & Nucleotide & blastx\tabularnewline
-Nucleotide & Protein & tblastn\tabularnewline
-\end{tabular}
-\par\end{center}
-
-Finally, it is also possible to use \textbf{blast\_seq} for blasting
-sequences agains a preformatted genome using the -\/-genome switch
-instead of the -\/-database switch:
-
-\begin{lyxcode}
-...~|~blast\_seq~-{}-genome=<genome>
-\end{lyxcode}
-
-\subsection{How to use Vmatch for sequence search?\label{sub:How-to-use-Vmatch}}
-
-The powerful suffix array software package Vmatch%
-\footnote{\url{http://www.vmatch.de/}%
-} can be used for exact mapping of sequences against indexed genomes
-using the biotool \textbf{vmatch\_seq}, which will e.g. map 700000
-ESTs to the human genome locating all 160 mio hits in less than an
-hour.
-
-\begin{lyxcode}
-...~|~vmatch\_seq~-{}-genome=<genome>
-\end{lyxcode}
-Only nucleotide sequences and sequences longer than 11 nucleotides
-will be mapped. The resulting SCORE key will hold the number of genome
-matches of a given sequence (multi-mappers).
-
-
-\subsection{How to find all matches between sequences?\label{sub:How-to-find-matches}}
-
-All matches between two sequences can be determined with the biotool
-\textbf{match\_seq}. The match finding engine underneath the hood
-of \textbf{match\_seq} is the super fast suffix tree program MUMmer%
-\footnote{\url{http://mummer.sourceforge.net/}%
-}, which will locate all forward and reverse matches between huge sequences
-in a matter of minutes (if the repeat count is not too high and if
-the word size used is appropriate). Matching two \emph{Helicobacter
-pylori} genomes (1.7Mbp) takes around 10 seconds:
-
-\begin{lyxcode}
-...~|~match\_seq~-{}-word\_size=20~-{}-direction=both
-\end{lyxcode}
-The output from \textbf{match\_seq} can be used to generate a dot
-plot with \textbf{plot\_matches} (see~\ref{sub:How-to-generate-dotplot}).
-
-
-\subsection{How to align sequences?\label{sub:How-to-align}}
-
-Sequences in the stream can be aligned with the \textbf{align\_seq}
-biotool that uses Muscle%
-\footnote{\url{http://www.drive5.com/muscle/muscle.html}%
-} as aligment engine. Currently you cannot change any of the Muscle
-alignment parameters and \textbf{align\_seq} will create an alignment
-based on the defaults (which are really good!):
-
-\begin{lyxcode}
-...~|~align\_seq
-\end{lyxcode}
-The aligned output can be written to file in FASTA format using \textbf{write\_fasta}
-(see~\ref{sub:How-to-write-fasta}) or in pretty text using \textbf{write\_align}
-(see~\ref{sub:How-to-write-alignment}).
-
-
-\subsection{How to create a weight matrix?}
-
-If you want a weight matrix to show the sequence composition of a
-stack of sequences you can use the biotool create\_weight\_matrix:
-
-\begin{lyxcode}
-...~|~create\_weight\_matrix
-\end{lyxcode}
-The result can be output in percent using the -\/-percent switch:
-
-\begin{lyxcode}
-...~|~create\_weight\_matrix~-{}-percent
-\end{lyxcode}
-The weight matrix can be written as tabular output with \textbf{write\_tab}
-(see~\ref{sub:How-to-write-tab}) after removeing the records containing
-SEQ with \textbf{grab} (see~\ref{sub:How-to-grab}):
-
-\begin{lyxcode}
-...~|~create\_weight\_matrix~|~grab~-{}-invert~-{}-keys=SEQ~-{}-keys\_only
-
-|~write\_tab~-{}-no\_stream
-\end{lyxcode}
-The V0 column will hold the residue, while the rest of the columns
-will hold the frequencies for each sequence position.
-
-
-\section{Plotting}
-
-There exists several biotools for plotting. Some of these are based
-on GNUplot%
-\footnote{\url{http://www.gnuplot.info/}%
-}, which is an extremely powerful platform to generate all sorts of
-plots and even though GNUplot has quite a steep learning curve, the
-biotools utilizing GNUplot are simple to use. GNUplot is able to output
-a lot of different formats (called terminals in GNUplot), but the
-biotools focusses on three formats only:
-
-\begin{enumerate}
-\item The 'dumb' terminal is default to the GNUplot based biotools and will
-output a plot in crude ASCII text (Fig.~\ref{fig:Dumb-terminal}).
-This is quite nice for a quick and dirty plot to get an overview of
-your data .
-\item The 'post' or 'postscript' terminal output postscript code which is
-publication grade graphics that can be viewed with applications such
-as Ghostview, Photoshop, and Preview.
-\item The 'svg' terminal output's scalable vector graphics (SVG) which is
-a vector based format. SVG is great because you can edit the resulting
-plot using Photoshop or Inkscape%
-\footnote{Inkscape is a really handy drawing program that is free and open source.
-Availble at \url{http://www.inkscape.org}%
-} if you want to add additional labels, captions, arrows, and so on
-and then save the result in different formats, such as postscript
-without loosing resolution.
-\end{enumerate}
-The biotools for plotting that are not based on GNUplot only output
-SVG (that may change in the future).
-
-%
-\begin{figure}
-\noindent \begin{centering}
-\includegraphics[width=12cm]{lendist_ascii}
-\par\end{centering}
-
-\caption{\label{fig:Dumb-terminal}Dumb terminal}
-
-
-\begin{quote}
-The output of a length distribution plot in the default 'dumb terminal'
-to the terminal window.
-\end{quote}
-
-\end{figure}
-
-
-
-\subsection{How to plot a histogram?\label{How-to-plot-histogram}}
-
-A generic histogram for a given value can be plotted with the biotool
-\textbf{plot\_histogram} (Fig.~\ref{fig:Histogram}):
-
-\begin{lyxcode}
-...~|~plot\_histogram~-{}-key=TISSUE~-{}-no\_stream
-\end{lyxcode}
-(Figure missing)
-
-\noindent \begin{flushleft}
-%
-\begin{figure}
-\noindent \begin{centering}
-\includegraphics[width=12cm]{histogram}
-\par\end{centering}
-
-\caption{\label{fig:Histogram}Histogram}
-
-\end{figure}
-
-\par\end{flushleft}
-
-
-\subsection{How to plot a length distribution?\label{sub:How-to-plot-lendist}}
-
-Plotting of length distributions, weather sequence lengths, patterns
-lengths, hit lengths, \emph{etc.} is a really handy thing and can
-be done with the the biotool \textbf{plot\_lendist}. If you have a
-file with FASTA entries and want to plot the length distribution you
-do it like this:
-
-\begin{lyxcode}
-read\_fasta~-{}-data\_in=<file>~|~length\_seq
-
-|~plot\_lendist~-{}-key=SEQ\_LEN~-{}-no\_stream
-\end{lyxcode}
-The result will be written to the default dumb terminal and will look
-like Fig.~\ref{fig:Dumb-terminal}.
-
-If you instead want the result in postscript format you can do:
-
-\begin{lyxcode}
-...~|~plot\_lendist~-{}-key=SEQ\_LEN~-{}-terminal=post~-{}-result\_out=file.ps
-\end{lyxcode}
-That will generate the plot and save it to file, but not interrupt
-the data stream which can then be used in further analysis. You can
-also save the plot implicetly using '>', however, it is then important
-to terminate the stream with the -\/-no\_stream switch:
-
-\begin{lyxcode}
-...~|~plot\_lendist~-{}-key=SEQ\_LEN~-{}-terminal=post~-{}-no\_stream~>~file.ps
-\end{lyxcode}
-The resulting plot can be seen in Fig.~\ref{fig:Length-distribution}.
-
-%
-\begin{figure}
-
-
-\noindent \begin{centering}
-\includegraphics[width=12cm]{lendist}
-\par\end{centering}
-
-\caption{\label{fig:Length-distribution}Length distribution}
-
-
-\begin{quote}
-Length distribution of 630 piRNA like RNAs.
-\end{quote}
-
-\end{figure}
-
-
-
-\subsection{How to plot a chromosome distribution?\label{sub:How-to-plot-chrdist}}
-
-If you have the result of a sequence search against a multi chromosome
-genome, it is very practical to be able to plot the distribution of
-search hits on the different chromosomes. This can be done with \textbf{plot\_chrdist}:
-
-\begin{lyxcode}
-read\_fasta~-{}-data\_in=<file>~|~blat\_genome~|~plot\_chrdist~-{}-no\_stream
-\end{lyxcode}
-The above example will result in a crude plot using the 'dumb' terminal,
-and if you want to mess around with the results from the BLAT search
-you probably want to save the result to file first (see~\ref{sub:How-to-write-PSL}).
-To plot the chromosome distribution from the saved search result you
-can do:
-
-\begin{lyxcode}
-read\_bed~-{}-data\_in=file.bed~|~plot\_chrdist~-{}-terminal=post~-{}-result\_out=plot.ps
-\end{lyxcode}
-That will result in the output show in Fig.~\ref{fig:Chromosome-distribution}.
-
-%
-\begin{figure}
-
-
-\noindent \begin{centering}
-\includegraphics[angle=90,width=12cm]{chrdist}
-\par\end{centering}
-
-\caption{\label{fig:Chromosome-distribution}Chromosome distribution}
-
-\end{figure}
-
-
-
-\subsection{How to generate a dotplot?\label{sub:How-to-generate-dotplot}}
-
-A dotplot is a powerful way to get an overview of the size and location
-of sequence insertions, deletions, and duplications between two sequences.
-Generating a dotplot with biotools is a two step process where you
-initially find all matches between two sequences using the tool \textbf{match\_seq}
-(see~\ref{sub:How-to-find-matches}) and plot the resulting matches
-with \textbf{plot\_matches}. Matching and plotting two \emph{Helicobacter
-pylori} genomes (1.7Mbp) takes around 10 seconds:
-
-\begin{lyxcode}
-...~|~match\_seq~|~plot\_matches~-{}-terminal=post~-{}-result\_out=plot.ps
-\end{lyxcode}
-The resulting dotplot is in Fig.~\ref{fig:Dotplot}.
-
-%
-\begin{figure}
-\noindent \begin{centering}
-\includegraphics[width=12cm]{dotplot}
-\par\end{centering}
-
-\caption{\label{fig:Dotplot}Dotplot}
-
-
-\begin{quote}
-Forward matches are displayed in green while reverse matches are displayed
-in red.
-\end{quote}
-
-\end{figure}
-
-
-
-\subsection{How to plot a sequence logo?}
-
-Sequence logos can be generate with \textbf{plot\_seqlogo}. The sequnce
-type is determined automagically and an entropy scale of 2 bits and
-4 bits is used for nucleotide and peptide sequences, respectively%
-\footnote{\url{http://www.ccrnp.ncifcrf.gov/~toms/paper/hawaii/latex/node5.html}%
-}.
-
-\begin{lyxcode}
-...~|~plot\_seqlogo~-{}-no\_stream~-{}-result\_out=seqlogo.svg
-\end{lyxcode}
-An example of a sequence logo can be seen in Fig.~\ref{fig:Sequence-logo}.
-
-%
-\begin{figure}
-\noindent \begin{centering}
-\includegraphics[width=12cm]{seqlogo}
-\par\end{centering}
-
-\caption{\label{fig:Sequence-logo}Sequence logo}
-
-\end{figure}
-
-
-
-\subsection{How to plot a karyogram?\label{sub:How-to-plot-karyogram}}
-
-To plot search hits on genomes use \textbf{plot\_karyogram}, which
-will output a nice karyogram in SVG graphics:
-
-\begin{lyxcode}
-...~|~plot\_karyogram~-{}-result\_out=karyogram.svg
-\end{lyxcode}
-The banding data is taken from the UCSC genome browser database and
-currently only Human and Mouse is supported. Fig.~\ref{fig:Karyogram}
-shows the distribution of piRNA like RNAs matched to the Human genome.
-
-%
-\begin{figure}
-\noindent \begin{centering}
-\includegraphics[width=12cm]{karyogram}
-\par\end{centering}
-
-\caption{\label{fig:Karyogram}Karyogram}
-
-
-\begin{quote}
-Hits from a search of piRNA like RNAs in the Human genome is displayed
-as short horizontal bars.
-\end{quote}
-
-\end{figure}
-
-
-
-\section{Uploading Results}
-
-
-\subsection{How do I display my results in the UCSC Genome Browser?}
-
-Results from the list of biotools below can be uploaded directly to
-a local mirror of the UCSC Genome Browser using the biotool \textbf{upload\_to\_ucsc}:
-
-\begin{itemize}
-\item patscan\_seq \eqref{sub:How-to-use-patscan}
-\item blat\_seq \eqref{sub:How-to-use-BLAT}
-\item blast\_seq \eqref{sub:How-to-use-BLAST}
-\item vmatch\_seq \eqref{sub:How-to-use-Vmatch}
-\end{itemize}
-The syntax for uploading data the most simple way requires two mandatory
-switches: -\/-database, which is the UCSC database name (such as
-hg18, mm9, etc.) and-\/-table which should be the users initials
-followed by an underscore and a short description of the data:
-
-\begin{lyxcode}
-...~|~upload\_to\_ucsc~-{}-database=hg18~-{}-table=mah\_snoRNAs
-\end{lyxcode}
-The \textbf{upload\_to\_ucsc} biotool modifies the users \textasciitilde{}/ucsc/my\_tracks.ra
-file automagically (a backup is created with the name \textasciitilde{}/ucsc/my\_tracks.ra\textasciitilde{})
-with default values that can be overridden using the following switches:
-
-\begin{itemize}
-\item -\/-short\_label - Short label for track - Default=database->table
-\item -\/-long\_label - Long label for track - Default=database->table
-\item -\/-group - Track group name - Default=<user name as defined in env>
-\item -\/-priority - Track display priority - Default=1
-\item -\/-color - Track color - Default=147,73,42
-\item -\/-chunk\_size - Chunks for loading - Default=10000000
-\item -\/-visibility - Track visibility - Default=pack
-\end{itemize}
-Also, data in BED or PSL format can be uploaded with \textbf{upload\_to\_ucsc}
-as long as these reference to genomes and chromosomes existing in
-the UCSC Genome Browser:
-
-\begin{lyxcode}
-read\_bed~-{}-data\_in=<bed~file>~|~upload\_to\_ucsc~...
-
-
-
-read\_psl~-{}-data\_in=<psl~file>~|~upload\_to\_ucsc~...
-\end{lyxcode}
-
-\section{Trouble shooting}
-
-Shoot the messenger!
-
-\appendix
-
-\section{Keys\label{sec:Keys}}
-
-HIT
-
-HIT\_BEG
-
-HIT\_END
-
-HIT\_LEN
-
-HIT\_NAME
-
-PATTERN
-
-
-\section{Switches\label{sec:Switches}}
-
--\/-stream\_in
-
--\/-stream\_out
-
--\/-no\_stream
-
--\/-data\_in
-
--\/-result\_out
-
--\/-num
-
-
-\section{scan\_for\_matches README\label{sec:scan_for_matches-README}}
-
-\begin{lyxcode}
-~~~~~~~~~~~~~~~~~~~~~~~~~~scan\_for\_matches:
-
-~~~~A~Program~to~Scan~Nucleotide~or~Protein~Sequences~for~Matching~Patterns
-
-~~~~~~~~~~~~~~~~~~~~~~~~Ross~Overbeek
-
-~~~~~~~~~~~~~~~~~~~~~~~~MCS
-
-~~~~~~~~~~~~~~~~~~~~~~~~Argonne~National~Laboratory
-
-~~~~~~~~~~~~~~~~~~~~~~~~Argonne,~IL~60439
-
-~~~~~~~~~~~~~~~~~~~~~~~~USA
-
-Scan\_for\_matches~is~a~utility~that~we~have~written~to~search~for
-
-patterns~in~DNA~and~protein~sequences.~~I~wrote~most~of~the~code,
-
-although~David~Joerg~and~Morgan~Price~wrote~sections~of~an
-
-earlier~version.~~The~whole~notion~of~pattern~matching~has~a~rich
-
-history,~and~we~borrowed~liberally~from~many~sources.~~However,~it~is
-
-worth~noting~that~we~were~strongly~influenced~by~the~elegant~tools
-
-developed~and~distributed~by~David~Searls.~~My~intent~is~to~make~the
-
-existing~tool~available~to~anyone~in~the~research~community~that~might
-
-find~it~useful.~~I~will~continue~to~try~to~fix~bugs~and~make~suggested
-
-enhancements,~at~least~until~I~feel~that~a~superior~tool~exists.
-
-Hence,~I~would~appreciate~it~if~all~bug~reports~and~suggestions~are
-
-directed~to~me~at~Overbeek@mcs.anl.gov.~~
-
-I~will~try~to~log~all~bug~fixes~and~report~them~to~users~that~send~me
-
-their~email~addresses.~~I~do~not~require~that~you~give~me~your~name
-
-and~address.~~However,~if~you~do~give~it~to~me,~I~will~try~to~notify
-
-you~of~serious~problems~as~they~are~discovered.
-
-Getting~Started:
-
-~~~~The~distribution~should~contain~at~least~the~following~programs:
-
-~~~~~~~~~~~~~~~~README~~~~~~~~~~~~~~~~~~-~~~~~This~document
-
-~~~~~~~~~~~~~~~~ggpunit.c~~~~~~~~~~~~~~~-~~~~~One~of~the~two~source~files
-
-~~~~~~~~~~~~~~~~scan\_for\_matches.c~~~~~~-~~~~~The~second~source~file
-
-~~~~~~~~~~~~~~~~
-
-~~~~~~~~~~~~~~~~run\_tests~~~~~~~~~~~~~~~-~~~~~A~perl~script~to~test~things
-
-~~~~~~~~~~~~~~~~show\_hits~~~~~~~~~~~~~~~-~~~~~A~handy~perl~script
-
-~~~~~~~~~~~~~~~~test\_dna\_input~~~~~~~~~~-~~~~~Test~sequences~for~DNA
-
-~~~~~~~~~~~~~~~~test\_dna\_patterns~~~~~~~-~~~~~Test~patterns~for~DNA~scan
-
-~~~~~~~~~~~~~~~~test\_output~~~~~~~~~~~~~-~~~~~Desired~output~from~test
-
-~~~~~~~~~~~~~~~~test\_prot\_input~~~~~~~~~-~~~~~Test~protein~sequences
-
-~~~~~~~~~~~~~~~~test\_prot\_patterns~~~~~~-~~~~~Test~patterns~for~proteins
-
-~~~~~~~~~~~~~~~~testit~~~~~~~~~~~~~~~~~~-~~~~~a~perl~script~used~for~test
-
-~~~~Only~the~first~three~files~are~required.~~The~others~are~useful,
-
-~~~~but~only~if~you~have~Perl~installed~on~your~system.~~If~you~do
-
-~~~~have~Perl,~I~suggest~that~you~type
-
-~~~~~~~~
-
-~~~~~~~~~~~~~~~~which~perl
-
-~~~~to~find~out~where~it~installed.~~On~my~system,~I~get~the~following
-
-~~~~response:
-
-~~~~~~~~
-
-~~~~~~~~~~~~~~~~clone\%~which~perl
-
-~~~~~~~~~~~~~~~~/usr/local/bin/perl
-
-~~~~indicating~that~Perl~is~installed~in~/usr/local/bin.~~Anyway,~once
-
-~~~~you~know~where~it~is~installed,~edit~the~first~line~of~files~
-
-~~~~~~~~testit
-
-~~~~~~~~show\_hits
-
-~~~~replacing~/usr/local/bin/perl~with~the~appropriate~location.~~I
-
-~~~~will~assume~that~you~can~do~this,~although~it~is~not~critical~(it
-
-~~~~is~needed~only~to~test~the~installation~and~to~use~the~\char`\"{}show\_hits\char`\"{}
-
-~~~~utility).~~Perl~is~not~required~to~actually~install~and~run
-
-~~~~scan\_for\_matches.~
-
-~~~~If~you~do~not~have~Perl,~I~suggest~you~get~it~and~install~it~(it
-
-~~~~is~a~wonderful~utility).~~Information~about~Perl~and~how~to~get~it
-
-~~~~can~be~found~in~the~book~\char`\"{}Programming~Perl\char`\"{}~by~Larry~Wall~and
-
-~~~~Randall~L.~Schwartz,~published~by~O'Reilly~\&~Associates,~Inc.
-
-~~~~To~get~started,~you~will~need~to~compile~the~program.~~~I~do~this
-
-~~~~using~
-
-~~~~~~~~gcc~-O~-o~scan\_for\_matches~~ggpunit.c~scan\_for\_matches.c
-
-~~~~If~you~do~not~use~GNU~C,~use~
-
-~~~~~~~~cc~-O~-DCC~-o~scan\_for\_matches~~ggpunit.c~scan\_for\_matches.c
-
-~~~~which~works~on~my~Sun.~~
-
-~~~~Once~you~have~compiled~scan\_for\_matches,~you~can~verify~that~it
-
-~~~~works~with
-
-~~~~~~~~clone\%~run\_tests~tmp
-
-~~~~~~~~clone\%~diff~tmp~test\_output
-
-~~~~You~may~get~a~few~strange~lines~of~the~sort
-
-~~~~~~~~clone\%~run\_tests~tmp
-
-~~~~~~~~rm:~tmp:~No~such~file~or~directory
-
-~~~~~~~~clone\%~diff~tmp~test\_output
-
-~~~~These~should~cause~no~concern.~~However,~if~the~\char`\"{}diff\char`\"{}~shows~that
-
-~~~~tmp~and~test\_output~are~different,~contact~me~(you~have~a
-
-~~~~problem).~
-
-~~~~You~should~now~be~able~to~use~scan\_for\_matches~by~following~the
-
-~~~~instructions~given~below~(which~is~all~the~normal~user~should~have
-
-~~~~to~understand,~once~things~are~installed~properly).
-
-~==============================================================
-
-How~to~run~scan\_for\_matches:
-
-~~~~To~run~the~program,~you~type~need~to~create~two~files
-
-~~~~1.~~the~first~file~contains~the~pattern~you~wish~to~scan~for;~I'll
-
-~~~~~~~~call~this~file~pat\_file~in~what~follows~(but~any~name~is~ok)
-
-~~~~2.~~the~second~file~contains~a~set~of~sequences~to~scan.~~These
-
-~~~~~~~~should~be~in~\char`\"{}fasta~format\char`\"{}.~~Just~look~at~the~contents~of
-
-~~~~~~~~test\_dna\_input~to~see~examples~of~this~format.~~Basically,
-
-~~~~~~~~each~sequence~begins~with~a~line~of~the~form
-
-~~~~~~~~~~~>sequence\_id
-
-~~~~~~~~and~is~followed~by~one~or~more~lines~containing~the~sequence.
-
-~~~~Once~these~files~have~been~created,~you~just~use
-
-~~~~~~~~scan\_for\_matches~pat\_file~<~input\_file
-
-~~~~to~scan~all~of~the~input~sequences~for~the~given~pattern.~~As~an
-
-~~~~example,~suppose~that~pat\_file~contains~a~single~line~of~the~form
-
-~~~~~~~~~~~~~~~~p1=4...7~3...8~\textasciitilde{}p1
-
-~~~~Then,
-
-~~~~~~~~~~~~~~~~scan\_for\_matches~pat\_file~<~test\_dna\_input
-
-~~~~should~produce~two~\char`\"{}hits\char`\"{}.~~When~I~run~this~on~my~machine,~I~get
-
-~~~~~~~~clone\%~scan\_for\_matches~pat\_file~<~test\_dna\_input
-
-~~~~~~~~>tst1:{[}6,27]
-
-~~~~~~~~cguaacc~ggttaacc~gguuacg~
-
-~~~~~~~~>tst2:{[}6,27]
-
-~~~~~~~~CGUAACC~GGTTAACC~GGUUACG~
-
-~~~~~~~~clone\%~
-
-Simple~Patterns~Built~by~Matching~Ranges~and~Reverse~Complements
-
-~~~~Let~me~first~explain~this~simple~pattern:
-
-~~~~~~~~~~~~~~~~
-
-~~~~~~~~~~~~~~~~p1=4...7~3...8~\textasciitilde{}p1
-
-~~~~The~pattern~consists~of~three~\char`\"{}pattern~units\char`\"{}~separated~by~spaces.
-
-~~~~The~first~pattern~unit~is
-
-~~~~~~~~~~~~~~~~p1=4...7
-
-~~~~which~means~\char`\"{}match~4~to~7~characters~and~call~them~p1\char`\"{}.~~The
-
-~~~~second~pattern~unit~is
-
-~~~~~~~~~~~~~~~~3...8
-
-~~~~which~means~\char`\"{}then~match~3~to~8~characters\char`\"{}.~~The~last~pattern~unit
-
-~~~~is~
-
-~~~~~~~~~~~~~~~~\textasciitilde{}p1
-
-~~~~which~means~\char`\"{}match~the~reverse~complement~of~p1\char`\"{}.~~The~first
-
-~~~~reported~hit~is~shown~as
-
-~~~~~~~~>tst1:{[}6,27]
-
-~~~~~~~~cguaacc~ggttaacc~gguuacg~
-
-~~~~which~states~that~characters~6~through~27~of~sequence~tst1~were
-
-~~~~matched.~~\char`\"{}cguaac\char`\"{}~matched~the~first~pattern~unit,~\char`\"{}ggttaacc\char`\"{}~the
-
-~~~~second,~and~\char`\"{}gguuacg\char`\"{}~the~third.~~This~is~an~example~of~a~common
-
-~~~~type~of~pattern~used~to~search~for~sections~of~DNA~or~RNA~that
-
-~~~~would~fold~into~a~hairpin~loop.
-
-Searching~Both~Strands
-
-~~~~Now~for~a~short~aside:~scan\_for\_matches~only~searched~the
-
-~~~~sequences~in~the~input~file;~it~did~not~search~the~opposite
-
-~~~~strand.~~With~a~pattern~of~the~sort~we~just~used,~there~is~not
-
-~~~~need~o~search~the~opposite~strand.~~However,~it~is~normally~the
-
-~~~~case~that~you~will~wish~to~search~both~the~sequence~and~the
-
-~~~~opposite~strand~(i.e.,~the~reverse~complement~of~the~sequence).
-
-~~~~To~do~that,~you~would~just~use~the~\char`\"{}-c\char`\"{}~command~line.~~For~example,
-
-~~~~~~~~scan\_for\_matches~-c~pat\_file~<~test\_dna\_input
-
-~~~~Hits~on~the~opposite~strand~will~show~a~beginning~location~greater
-
-~~~~than~te~end~location~of~the~match.
-
-Defining~Pairing~Rules~and~Allowing~Mismatches,~Insertions,~and~Deletions
-
-~~~~Let~us~stop~now~and~ask~\char`\"{}What~additional~features~would~one~need~to
-
-~~~~really~find~the~kinds~of~loop~structures~that~characterize~tRNAs,
-
-~~~~rRNAs,~and~so~forth?\char`\"{}~~I~can~immediately~think~of~two:
-
-~~~~~~~~a)~you~will~need~to~be~able~to~allow~non-standard~pairings
-
-~~~~~~~~~~~(those~other~than~G-C~and~A-U),~and
-
-~~~~~~~~b)~you~will~need~to~be~able~to~tolerate~some~number~of
-
-~~~~~~~~~~~mismatches~and~bulges.
-
-~~~~~~~~
-
-~~~~Let~me~first~show~you~how~to~handle~non-standard~\char`\"{}rules~for
-
-~~~~pairing~in~reverse~complements\char`\"{}.~~Consider~the~following~pattern,
-
-~~~~which~I~show~as~two~line~(you~may~use~as~many~lines~as~you~like~in
-
-~~~~forming~a~pattern,~although~you~can~only~break~a~pattern~at~points
-
-~~~~where~space~would~be~legal):
-
-~~~~~~~~~~~~r1=\{au,ua,gc,cg,gu,ug,ga,ag\}~
-
-~~~~~~~~~~~~p1=2...3~0...4~p2=2...5~1...5~r1\textasciitilde{}p2~0...4~\textasciitilde{}p1~~~~~~~~
-
-~~~~The~first~\char`\"{}pattern~unit\char`\"{}~does~not~actually~match~anything;~rather,
-
-~~~~it~defines~a~\char`\"{}pairing~rule\char`\"{}~in~which~standard~pairings~are
-
-~~~~allowed,~as~well~as~G-A~and~A-G~(in~case~you~wondered,~Us~and~Ts
-
-~~~~and~upper~and~lower~case~can~be~used~interchangably;~for~example
-
-~~~~r1=\{AT,UA,gc,cg\}~could~be~used~to~define~the~\char`\"{}standard~rule\char`\"{}~for
-
-~~~~pairings).~~The~second~line~consists~of~six~pattern~units~which
-
-~~~~may~be~interpreted~as~follows:
-
-~~~~~~~~~~~~p1=2...3~~~~~match~2~or~3~characters~(call~it~p1)
-
-~~~~~~~~~~~~0...4~~~~~~~~match~0~to~4~characters
-
-~~~~~~~~~~~~p2=2...5~~~~~match~2~to~5~characters~(call~it~p2)
-
-~~~~~~~~~~~~1...5~~~~~~~~match~1~to~5~characters
-
-~~~~~~~~~~~~r1\textasciitilde{}p2~~~~~~~~match~the~reverse~complement~of~p2,
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~allowing~G-A~and~A-G~pairs
-
-~~~~~~~~~~~~0...4~~~~~~~~match~0~to~4~characters~~~~~~~~
-
-~~~~~~~~~~~~\textasciitilde{}p1~~~~~~~~~~match~the~reverse~complement~of~p1
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~allowing~only~G-C,~C-G,~A-T,~and~T-A~pairs
-
-~~~~Thus,~r1\textasciitilde{}p2~means~\char`\"{}match~the~reverse~complement~of~p2~using~rule~r1\char`\"{}.
-
-~~~~Now~let~us~consider~the~issue~of~tolerating~mismatches~and~bulges.
-
-~~~~You~may~add~a~\char`\"{}qualifier\char`\"{}~to~the~pattern~unit~that~gives~the
-
-~~~~tolerable~number~of~\char`\"{}mismatches,~deletions,~and~insertions\char`\"{}.
-
-~~~~Thus,
-
-~~~~~~~~~~~~~~~~p1=10...10~3...8~\textasciitilde{}p1{[}1,2,1]
-
-~~~~means~that~the~third~pattern~unit~must~match~10~characters,
-
-~~~~allowing~one~\char`\"{}mismatch\char`\"{}~(a~pairing~other~than~G-C,~C-G,~A-T,~or
-
-~~~~T-A),~two~deletions~(a~deletion~is~a~character~that~occurs~in~p1,
-
-~~~~but~has~been~\char`\"{}deleted\char`\"{}~from~the~string~matched~by~\textasciitilde{}p1),~and~one
-
-~~~~insertion~(an~\char`\"{}insertion\char`\"{}~is~a~character~that~occurs~in~the~string
-
-~~~~matched~by~\textasciitilde{}p1,~but~not~for~which~no~corresponding~character
-
-~~~~occurs~in~p1).~~In~this~case,~the~pattern~would~match
-
-~~~~~~~~~~~~~~ACGTACGTAC~GGGGGGGG~GCGTTACCT
-
-~~~~which~is,~you~must~admit,~a~fairly~weak~loop.~~It~is~common~to
-
-~~~~allow~mismatches,~but~you~will~find~yourself~using~insertions~and
-
-~~~~deletions~much~more~rarely.~~In~any~event,~you~should~note~that
-
-~~~~allowing~mismatches,~insertions,~and~deletions~does~force~the
-
-~~~~program~to~try~many~additional~possible~pairings,~so~it~does~slow
-
-~~~~things~down~a~bit.
-
-How~Patterns~Are~Matched
-
-~~~~Now~is~as~good~a~time~as~any~to~discuss~the~basic~flow~of~control
-
-~~~~when~matching~patterns.~~Recall~that~a~\char`\"{}pattern\char`\"{}~is~a~sequence~of
-
-~~~~\char`\"{}pattern~units\char`\"{}.~~Suppose~that~the~pattern~units~were
-
-~~~~~~~~u1~u2~u3~u4~...~un
-
-~~~~The~scan~of~a~sequence~S~begins~by~setting~the~current~position
-
-~~~~to~1.~~Then,~an~attempt~is~made~to~match~u1~starting~at~the
-
-~~~~current~position.~~Each~attempt~to~match~a~pattern~unit~can
-
-~~~~succeed~or~fail.~~If~it~succeeds,~then~an~attempt~is~made~to~match
-
-~~~~the~next~unit.~~If~it~fails,~then~an~attempt~is~made~to~find~an
-
-~~~~alternative~match~for~the~immediately~preceding~pattern~unit.~~If
-
-~~~~this~succeeds,~then~we~proceed~forward~again~to~the~next~unit.~~If
-
-~~~~it~fails~we~go~back~to~the~preceding~unit.~~This~process~is~called
-
-~~~~\char`\"{}backtracking\char`\"{}.~~If~there~are~no~previous~units,~then~the~current
-
-~~~~position~is~incremented~by~one,~and~everything~starts~again.~~This
-
-~~~~proceeds~until~either~the~current~position~goes~past~the~end~of
-
-~~~~the~sequence~or~all~of~the~pattern~units~succeed.~~On~success,
-
-~~~~scan\_for\_matches~reports~the~\char`\"{}hit\char`\"{},~the~current~position~is~set
-
-~~~~just~past~the~hit,~and~an~attempt~is~made~to~find~another~hit.
-
-~~~~If~you~wish~to~limit~the~scan~to~simply~finding~a~maximum~of,~say,
-
-~~~~10~hits,~you~can~use~the~-n~option~(-n~10~would~set~the~limit~to
-
-~~~~10~reported~hits).~~For~example,
-
-~~~~~~~~scan\_for\_matches~-c~-n~1~pat\_file~<~test\_dna\_input
-
-~~~~would~search~for~just~the~first~hit~(and~would~stop~searching~the
-
-~~~~current~sequences~or~any~that~follow~in~the~input~file).
-
-Searching~for~repeats:
-
-~~~~In~the~last~section,~I~discussed~almost~all~of~the~details
-
-~~~~required~to~allow~you~to~look~for~repeats.~~Consider~the~following
-
-~~~~set~of~patterns:
-
-~~~~~~~~p1=6...6~3...8~p1~~~(find~exact~6~character~repeat~separated
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~by~to~8~characters)
-
-~~~~~~~~p1=6...6~3..8~p1{[}1,0,0]~~~(allow~one~mismatch)
-
-~~~~~~~~p1=3...3~p1{[}1,0,0]~p1{[}1,0,0]~p1{[}1,0,0]~~
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~(match~12~characters~that~are~the~remains
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~of~a~3-character~sequence~occurring~4~times)
-
-~~~~~~~~~~~~~~~~
-
-~~~~~~~~p1=4...8~0...3~p2=6...8~p1~0...3~p2
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~(This~would~match~things~like
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ATCT~G~TCTTT~ATCT~TG~TCTTT
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~)
-
-Searching~for~particular~sequences:
-
-~~~~Occasionally,~one~wishes~to~match~a~specific,~known~sequence.
-
-~~~~In~such~a~case,~you~can~just~give~the~sequence~(along~with~an
-
-~~~~optional~statement~of~the~allowable~mismatches,~insertions,~and
-
-~~~~deletions).~~Thus,
-
-~~~~~~~~p1=6...8~GAGA~\textasciitilde{}p1~~~~(match~a~hairpin~with~GAGA~as~the~loop)
-
-~~~~~~~~RRRRYYYY~~~~~~~~~~~~~(match~4~purines~followed~by~4~pyrimidines)
-
-~~~~~~~~TATAA{[}1,0,0]~~~~~~~~~(match~TATAA,~allowing~1~mismatch)
-
-~~~~~~~~
-
-Matches~against~a~\char`\"{}weight~matrix\char`\"{}:
-
-~~~~I~will~conclude~my~examples~of~the~types~of~pattern~units
-
-~~~~available~for~matching~against~nucleotide~sequences~by~discussing~a
-
-~~~~crude~implemetation~of~matching~using~a~\char`\"{}weight~matrix\char`\"{}.~~While~I
-
-~~~~am~less~than~overwhelmed~with~the~syntax~that~I~chose,~I~think~that
-
-~~~~the~reader~should~be~aware~that~I~was~thinking~of~generating
-
-~~~~patterns~containing~such~pattern~units~automatically~from
-
-~~~~alignments~(and~did~not~really~plan~on~typing~such~things~in~by
-
-~~~~hand~very~often).~~Anyway,~suppose~that~you~wanted~to~match~a
-
-~~~~sequence~of~eight~characters.~~The~\char`\"{}consensus\char`\"{}~of~these~eight
-
-~~~~characters~is~GRCACCGS,~but~the~actual~\char`\"{}frequencies~of~occurrence\char`\"{}
-
-~~~~are~given~in~the~matrix~below.~~Thus,~the~first~character~is~an~A
-
-~~~~16\%~the~time~and~a~G~84\%~of~the~time.~~The~second~is~an~A~57\%~of
-
-~~~~the~time,~a~C~10\%~of~the~time,~a~G~29\%~of~the~time,~and~a~T~4\%~of
-
-~~~~the~time.~~
-
-~~~~~~~~~~~~~C1~~~~~C2~~~~C3~~~~C4~~~C5~~~~C6~~~~C7~~~~C8
-
-~~~~
-
-~~~~~~~A~~~~~16~~~~~57~~~~~0~~~~95~~~~0~~~~18~~~~~0~~~~~0
-
-~~~~~~~C~~~~~~0~~~~~10~~~~80~~~~~0~~100~~~~60~~~~~0~~~~50
-
-~~~~~~~G~~~~~84~~~~~29~~~~~0~~~~~0~~~~0~~~~20~~~100~~~~50
-
-~~~~~~~T~~~~~~0~~~~~~4~~~~20~~~~~5~~~~0~~~~~2~~~~~0~~~~~0~~~
-
-~~~~
-
-~~~~One~could~use~the~following~pattern~unit~to~search~for~inexact
-
-~~~~matches~related~to~such~a~\char`\"{}weight~matrix\char`\"{}:
-
-~~~~~~~~\{(16,0,84,0),(57,10,29,4),(0,80,0,20),(95,0,0,5),
-
-~~~~~~~~~(0,100,0,0),(18,60,20,2),(0,0,100,0),(0,50,50,0)\}~>~450
-
-~~~~This~pattern~unit~will~attempt~to~match~exactly~eight~characters.
-
-~~~~For~each~character~in~the~sequence,~the~entry~in~the~corresponding
-
-~~~~tuple~is~added~to~an~accumulated~sum.~~If~the~sum~is~greater~than
-
-~~~~450,~the~match~succeeds;~else~it~fails.
-
-~~~~Recently,~this~feature~was~upgraded~to~allow~ranges.~~Thus,
-
-~~600~>~~\{(16,0,84,0),(57,10,29,4),(0,80,0,20),(95,0,0,5),
-
-~~~~~~~~~(0,100,0,0),(18,60,20,2),(0,0,100,0),(0,50,50,0)\}~>~450
-
-~~~~will~work,~as~well.
-
-Allowing~Alternatives:
-
-~~~~Very~occasionally,~you~may~wish~to~allow~alternative~pattern~units
-
-~~~~(i.e.,~\char`\"{}match~either~A~or~B\char`\"{}).~~You~can~do~this~using~something
-
-~~~~like
-
-~~~~~~~~~~~~~~~~(~GAGA~|~GCGCA)
-
-~~~~which~says~\char`\"{}match~either~GAGA~or~GCGCA\char`\"{}.~~You~may~take
-
-~~~~alternatives~of~a~list~of~pattern~units,~for~example
-
-~~~~~~~~(p1=3...3~3...8~\textasciitilde{}p1~|~p1=5...5~4...4~\textasciitilde{}p1~GGG)
-
-~~~~would~match~one~of~two~sequences~of~pattern~units.~~There~is~one
-
-~~~~clumsy~aspect~of~the~syntax:~to~match~a~list~of~alternatives,~you
-
-~~~~need~to~fully~the~request.~~Thus,
-
-~~~~~~~~(GAGA~|~(GCGCA~|~TTCGA))
-
-~~~~would~be~needed~to~try~the~three~alternatives.
-
-One~Minor~Extension
-
-~~~~Sometimes~a~pattern~will~contain~a~sequence~of~distinct~ranges,
-
-~~~~and~you~might~wish~to~limit~the~sum~of~the~lengths~of~the~matched
-
-~~~~subsequences.~~~For~example,~suppose~that~you~basically~wanted~to
-
-~~~~match~something~like
-
-~~~~ARRYYTT~p1=0...5~GCA{[}1,0,0]~p2=1...6~\textasciitilde{}p1~4...8~\textasciitilde{}p2~p3=4...10~CCT
-
-~~~~but~that~the~sum~of~the~lengths~of~p1,~p2,~and~p3~must~not~exceed
-
-~~~~eight~characters.~~To~do~this,~you~could~add~
-
-~~~~~~~~length(p1+p2+p3)~<~9
-
-~~~~as~the~last~pattern~unit.~~It~will~just~succeed~or~fail~(but~does
-
-~~~~not~actually~match~any~characters~in~the~sequence).
-
-~~~~
-
-Matching~Protein~Sequences
-
-~~~~Suppose~that~the~input~file~contains~protein~sequences.~~In~this
-
-~~~~case,~you~must~invoke~scan\_for\_matches~with~the~\char`\"{}-p\char`\"{}~option.~~You
-
-~~~~cannot~use~aspects~of~the~language~that~relate~directly~to
-
-~~~~nucleotide~sequences~(e.g.,~the~-c~command~line~option~or~pattern
-
-~~~~constructs~referring~to~the~reverse~complement~of~a~previously
-
-~~~~matched~unit).~~
-
-~~~~You~also~have~two~additional~constructs~that~allow~you~to~match
-
-~~~~either~\char`\"{}one~of~a~set~of~amino~acids\char`\"{}~or~\char`\"{}any~amino~acid~other~than
-
-~~~~those~a~given~set\char`\"{}.~~For~example,
-
-~~~~~~~~p1=0...4~any(HQD)~1...3~notany(HK)~p1
-
-~~~~would~successfully~match~a~string~like
-
-~~~~~~~~~~~YWV~D~AA~C~YWV
-
-Using~the~show\_hits~Utility
-
-~~~~When~viewing~a~large~set~of~complex~matches,~you~might~find~it
-
-~~~~convenient~to~post-process~the~scan\_for\_matches~output~to~get~a
-
-~~~~more~readable~version.~~We~provide~a~simple~post-processor~called
-
-~~~~\char`\"{}show\_hits\char`\"{}.~~To~see~its~effect,~just~pipe~the~output~of~a
-
-~~~~scan\_for\_matches~into~show\_hits:
-
-~~~~~Normal~Output:
-
-~~~~~~~~clone\%~scan\_for\_matches~-c~pat\_file~<~tmp
-
-~~~~~~~~>tst1:{[}1,28]
-
-~~~~~~~~gtacguaacc~~ggttaac~cgguuacgtac~
-
-~~~~~~~~>tst1:{[}28,1]
-
-~~~~~~~~gtacgtaacc~~ggttaac~cggttacgtac~
-
-~~~~~~~~>tst2:{[}2,31]
-
-~~~~~~~~CGTACGUAAC~C~GGTTAACC~GGUUACGTACG~
-
-~~~~~~~~>tst2:{[}31,2]
-
-~~~~~~~~CGTACGTAAC~C~GGTTAACC~GGTTACGTACG~
-
-~~~~~~~~>tst3:{[}3,32]
-
-~~~~~~~~gtacguaacc~g~gttaactt~cgguuacgtac~
-
-~~~~~~~~>tst3:{[}32,3]
-
-~~~~~~~~gtacgtaacc~g~aagttaac~cggttacgtac~
-
-~~~~~Piped~Through~show\_hits:
-
-~~~~
-
-~~~~~~~~clone\%~scan\_for\_matches~-c~pat\_file~<~tmp~|~show\_hits
-
-~~~~~~~~tst1:{[}1,28]:~~gtacguaacc~~~ggttaac~~cgguuacgtac
-
-~~~~~~~~tst1:{[}28,1]:~~gtacgtaacc~~~ggttaac~~cggttacgtac
-
-~~~~~~~~tst2:{[}2,31]:~~CGTACGUAAC~C~GGTTAACC~GGUUACGTACG
-
-~~~~~~~~tst2:{[}31,2]:~~CGTACGTAAC~C~GGTTAACC~GGTTACGTACG
-
-~~~~~~~~tst3:{[}3,32]:~~gtacguaacc~g~gttaactt~cgguuacgtac
-
-~~~~~~~~tst3:{[}32,3]:~~gtacgtaacc~g~aagttaac~cggttacgtac
-
-~~~~~~~~clone\%~
-
-~~~~Optionally,~you~can~specify~which~of~the~\char`\"{}fields\char`\"{}~in~the~matches
-
-~~~~you~wish~to~sort~on,~and~show\_hits~will~sort~them.~~The~field
-
-~~~~numbers~start~with~0.~~So,~you~might~get~something~like
-
-~~~~~~~~clone\%~scan\_for\_matches~-c~pat\_file~<~tmp~|~show\_hits~2~1
-
-~~~~~~~~tst2:{[}2,31]:~~CGTACGUAAC~C~GGTTAACC~GGUUACGTACG
-
-~~~~~~~~tst2:{[}31,2]:~~CGTACGTAAC~C~GGTTAACC~GGTTACGTACG
-
-~~~~~~~~tst3:{[}32,3]:~~gtacgtaacc~g~aagttaac~cggttacgtac
-
-~~~~~~~~tst1:{[}1,28]:~~gtacguaacc~~~ggttaac~~cgguuacgtac
-
-~~~~~~~~tst1:{[}28,1]:~~gtacgtaacc~~~ggttaac~~cggttacgtac
-
-~~~~~~~~tst3:{[}3,32]:~~gtacguaacc~g~gttaactt~cgguuacgtac
-
-~~~~~~~~clone\%~
-
-~~~~In~this~case,~the~hits~have~been~sorted~on~fields~2~and~1~(that~is,
-
-~~~~the~third~and~second~matched~subfields).
-
-~~~~show\_hits~is~just~one~possible~little~post-processor,~and~you
-
-~~~~might~well~wish~to~write~a~customized~one~for~yourself.
-
-Reducing~the~Cost~of~a~Search
-
-~~~~The~scan\_for\_matches~utility~uses~a~fairly~simple~search,~and~may
-
-~~~~consume~large~amounts~of~CPU~time~for~complex~patterns.~~Someday,
-
-~~~~I~may~decide~to~optimize~the~code.~~However,~until~then,~let~me
-
-~~~~mention~one~useful~technique.~~
-
-~~~~When~you~have~a~complex~pattern~that~includes~a~number~of~varying
-
-~~~~ranges,~imprecise~matches,~and~so~forth,~it~is~useful~to
-
-~~~~\char`\"{}pipeline\char`\"{}~matches.~~That~is,~form~a~simpler~pattern~that~can~be
-
-~~~~used~to~scan~through~a~large~database~extracting~sections~that
-
-~~~~might~be~matched~by~the~more~complex~pattern.~~Let~me~illustrate
-
-~~~~with~a~short~example.~~Suppose~that~you~really~wished~to~match~the
-
-~~~~pattern~
-
-~~~~p1=3...5~0...8~\textasciitilde{}p1{[}1,1,0]~p2=6...7~3...6~AGC~3...5~RYGC~\textasciitilde{}p2{[}1,0,0]
-
-~~~~In~this~case,~the~pattern~units~AGC~3...5~RYGC~can~be~used~to~rapidly
-
-~~~~constrain~the~overall~search.~~You~can~preprocess~the~overall
-
-~~~~database~using~the~pattern:
-
-~~~~~~~~~~31...31~AGC~3...5~RYGC~7...7
-
-~~~~Put~the~complex~pattern~in~pat\_file1~and~the~simpler~pattern~in
-
-~~~~pat\_file2.~~Then~use,
-
-~~~~~~~~scan\_for\_matches~-c~pat\_file2~<~nucleotide\_database~|
-
-~~~~~~~~scan\_for\_matches~pat\_file1
-
-~~~~The~output~will~show~things~like
-
-~~~~>seqid:{[}232,280]{[}2,47]
-
-~~~~matches~pieces
-
-~~~~Then,~the~actual~section~of~the~sequence~that~was~matched~can~be
-
-~~~~easily~computed~as~{[}233,278]~(remember,~the~positions~start~from
-
-~~~~1,~not~0).
-
-~~~~Let~me~finally~add,~you~should~do~a~few~short~experiments~to~see
-
-~~~~whether~or~not~such~pipelining~actually~improves~performance~-{}-~it
-
-~~~~is~not~always~obvious~where~the~time~is~going,~and~I~have
-
-~~~~sometimes~found~that~the~added~complexity~of~pipelining~actually
-
-~~~~slowed~things~up.~~It~gets~its~best~improvements~when~there~are
-
-~~~~exact~matches~of~more~than~just~a~few~characters~that~can~be
-
-~~~~rapidly~used~to~eliminate~large~sections~of~the~database.
-
-=============
-
-Additions:
-
-Feb~9,~1995:~~~the~pattern~units~\textasciicircum{}~and~\$~now~work~as~in~normal~regular
-
-~~~~~~~~~~~~~~~expressions.~~That~is
-
-~~~~~~~~~~~~~~~~~~~~~~~~TTF~\$
-
-~~~~~~~~~~~~~~~matches~only~TTF~at~the~end~of~the~string~and~
-
-~~~~~~~~~~~~~~~~~~~~~~~~\textasciicircum{}~TTF~
-
-~~~~~~~~~~~~~~~matches~only~an~initial~TTF
-
-~~~~~~~~~~~~~~~The~pattern~unit~
-
-~~~~~~~~~~~~~~~~~~~~~~~~<p1
-
-~~~~~~~~~~~~~~~matches~the~reverse~of~the~string~named~p1.~~That~is,
-
-~~~~~~~~~~~~~~~if~p1~matched~GCAT,~then~<p1~would~match~TACG.~~Thus,
-
-~~~~~~~~~~~~~~~~~~~p1=6...6~<p1
-
-~~~~~~~~~~~~~~~matches~a~real~palindrome~(not~the~biologically~common
-
-~~~~~~~~~~~~~~~meaning~of~\char`\"{}reverse~complement\char`\"{})
-
-
-\end{lyxcode}
-
-\end{document}
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- <g transform="translate(101.7,421.5)" style="stroke:none; fill:black; font-family:Arial; font-size:12.00; text-anchor:end">
- <text> 0</text>
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- <g transform="translate(101.7,378.0)" style="stroke:none; fill:black; font-family:Arial; font-size:12.00; text-anchor:end">
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- <g transform="translate(101.7,334.4)" style="stroke:none; fill:black; font-family:Arial; font-size:12.00; text-anchor:end">
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- <path d='M119.0,286.4 L110.0,286.4 M574.4,286.4 L583.4,286.4 '></path>
- <g transform="translate(101.7,290.9)" style="stroke:none; fill:black; font-family:Arial; font-size:12.00; text-anchor:end">
- <text> 600000</text>
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-<g style="fill:none; color:gray; stroke:currentColor; stroke-width:1.00; stroke-linecap:butt; stroke-linejoin:miter">
- <path d='M119.0,242.9 L574.4,242.9 '></path>
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-<g style="fill:none; color:black; stroke:currentColor; stroke-width:1.00; stroke-linecap:butt; stroke-linejoin:miter">
- <path d='M119.0,242.9 L110.0,242.9 M574.4,242.9 L583.4,242.9 '></path>
- <g transform="translate(101.7,247.4)" style="stroke:none; fill:black; font-family:Arial; font-size:12.00; text-anchor:end">
- <text> 800000</text>
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-<g style="fill:none; color:gray; stroke:currentColor; stroke-width:1.00; stroke-linecap:butt; stroke-linejoin:miter">
- <path d='M119.0,199.4 L574.4,199.4 '></path>
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- <path d='M119.0,199.4 L110.0,199.4 M574.4,199.4 L583.4,199.4 '></path>
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- <text> 1e+06</text>
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- <path d='M119.0,155.8 L110.0,155.8 M574.4,155.8 L583.4,155.8 '></path>
- <g transform="translate(101.7,160.3)" style="stroke:none; fill:black; font-family:Arial; font-size:12.00; text-anchor:end">
- <text> 1.2e+06</text>
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- <path d='M119.0,112.3 L574.4,112.3 '></path>
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- <path d='M119.0,112.3 L110.0,112.3 M574.4,112.3 L583.4,112.3 '></path>
- <g transform="translate(101.7,116.8)" style="stroke:none; fill:black; font-family:Arial; font-size:12.00; text-anchor:end">
- <text> 1.4e+06</text>
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- <path d='M119.0,68.8 L110.0,68.8 M574.4,68.8 L583.4,68.8 '></path>
- <g transform="translate(101.7,73.3)" style="stroke:none; fill:black; font-family:Arial; font-size:12.00; text-anchor:end">
- <text> 1.6e+06</text>
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- <g transform="translate(119.0,448.5)" style="stroke:none; fill:black; font-family:Arial; font-size:12.00; text-anchor:middle">
- <text> 0</text>
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- <path d='M174.4,417.0 L174.4,54.0 '></path>
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- <g transform="translate(174.4,448.5)" style="stroke:none; fill:black; font-family:Arial; font-size:12.00; text-anchor:middle">
- <text> 200000</text>
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- <g transform="translate(229.9,448.5)" style="stroke:none; fill:black; font-family:Arial; font-size:12.00; text-anchor:middle">
- <text> 400000</text>
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- <path d='M340.7,417.0 L340.7,426.0 M340.7,54.0 L340.7,45.0 '></path>
- <g transform="translate(340.7,448.5)" style="stroke:none; fill:black; font-family:Arial; font-size:12.00; text-anchor:middle">
- <text> 800000</text>
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- <path d='M396.1,417.0 L396.1,54.0 '></path>
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- <path d='M396.1,417.0 L396.1,426.0 M396.1,54.0 L396.1,45.0 '></path>
- <g transform="translate(396.1,448.5)" style="stroke:none; fill:black; font-family:Arial; font-size:12.00; text-anchor:middle">
- <text> 1e+06</text>
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- <path d='M451.6,417.0 L451.6,426.0 M451.6,54.0 L451.6,45.0 '></path>
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- <text> 1.2e+06</text>
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- <text> 1.4e+06</text>
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- <text> 1.6e+06</text>
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- L465.6,140.1 L465.7,140.1 L465.7,140.0 L465.8,140.0 L465.8,139.9 L465.9,139.9 L465.9,139.8 L466.0,139.8 L466.1,139.7 M466.2,139.7
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- L466.8,139.2 L466.8,139.1 M466.9,139.1 M466.9,215.0 M466.9,139.1 L466.9,139.0 M467.0,139.0 L467.1,138.9 L467.2,138.9 L467.2,138.8
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- M478.5,411.9 M478.5,146.3 M478.5,130.1 M478.5,344.7 M478.5,210.7 M478.5,415.8 M478.5,411.9 L478.5,411.8 M478.5,210.7 M478.5,130.1
- L478.6,130.1 M478.5,344.7 L478.6,344.7 M478.5,210.7 L478.6,210.7 M478.6,130.1 M478.6,344.7 M478.6,415.8 M478.6,365.0 M478.6,74.5
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- M478.6,210.6 M478.6,415.7 M478.6,130.0 L478.7,130.0 M478.6,344.6 L478.7,344.6 M478.6,210.6 L478.7,210.6 M478.7,130.0 M478.7,344.6
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- L479.5,129.3 M479.6,129.3 L479.6,129.2 L479.7,129.2 L479.7,129.1 L479.8,129.1 L479.8,129.0 L479.9,129.0 M480.0,129.0 L480.0,128.9
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- L480.6,128.5 L480.6,128.4 M480.7,128.4 L480.8,128.4 M480.8,128.3 L480.9,128.3 L480.9,128.2 L481.0,128.2 L481.0,128.1 L481.1,128.1
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- L482.4,127.0 L482.5,127.0 L482.6,126.9 M482.7,126.9 L482.7,126.8 L482.8,126.8 L482.8,126.7 M482.9,126.7 L482.9,126.6 L483.0,126.6
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- M485.5,124.6 L485.6,124.6 M485.5,393.9 M485.6,124.6 M485.6,124.5 L485.7,124.5 M485.7,124.4 L485.8,124.4 L485.9,124.4 M485.9,124.3
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- M486.6,123.8 L486.7,123.7 M486.8,123.6 L486.9,123.6 L486.9,123.5 L487.0,123.5 L487.0,123.4 M487.1,123.4 L487.1,123.3 L487.2,123.3
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- M489.2,121.8 M489.2,121.7 L489.3,121.7 M489.3,121.6 L489.4,121.6 L489.4,121.5 L489.5,121.5 M489.5,121.4 L489.6,121.4 L489.7,121.4
- L489.7,121.3 M489.7,407.4 M489.7,121.3 L489.8,121.3 M489.7,407.4 L489.8,407.3 M489.8,121.3 M489.9,120.9 L489.9,120.8 M490.0,120.8
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- M491.3,119.7 L491.4,119.7 L491.5,119.6 M491.7,119.5 L491.7,119.4 M491.7,208.9 M491.7,331.0 M491.8,119.4 L491.9,119.3 L492.0,119.3
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- L493.2,118.3 L493.3,118.3 M493.3,118.2 L493.4,118.2 L493.4,118.1 L493.5,118.1 L493.5,118.0 M493.6,118.0 L493.6,117.9 M493.7,117.9
- L493.8,117.9 L493.8,117.8 L493.9,117.8 L493.9,117.7 L494.0,117.7 M494.0,117.6 L494.1,117.6 M494.1,117.5 L494.2,117.5 L494.3,117.5
- M494.3,117.4 L494.4,117.4 L494.4,117.3 L494.5,117.3 L494.5,117.2 L494.6,117.2 M494.7,117.2 L494.7,117.1 L494.8,117.1 M494.8,117.0
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- L495.5,116.5 L495.6,116.4 L495.7,116.4 M495.7,116.3 L495.8,116.3 L495.8,116.2 L495.9,116.2 L495.9,116.1 M496.0,116.1 M496.1,116.1
- L496.1,116.0 M496.2,116.0 L496.2,115.9 L496.3,115.9 L496.3,115.8 M496.4,115.8 M496.4,115.7 L496.5,115.7 M496.6,115.7 L496.6,115.6
- L496.7,115.6 M496.7,115.5 M496.8,115.5 L496.8,115.4 L496.9,115.4 L497.0,115.3 M497.1,115.3 L497.1,115.2 M497.2,115.2 L497.2,115.1
- M497.3,115.1 M497.3,115.0 L497.4,115.0 L497.5,115.0 M497.5,114.9 L497.6,114.9 L497.6,114.8 L497.7,114.8 M497.7,114.7 M497.8,114.7
- M497.8,301.8 M497.8,114.7 M497.9,114.6 L498.0,114.6 M498.0,114.5 M498.1,114.5 M498.1,114.4 L498.2,114.4 L498.2,114.3 L498.3,114.3
- L498.4,114.3 L498.4,114.2 M498.5,114.2 M498.5,114.1 M498.6,114.1 M498.6,114.0 L498.7,114.0 L498.7,113.9 L498.8,113.9 M498.9,113.9
- L498.9,113.8 M499.0,113.8 M499.0,113.7 L499.1,113.7 L499.1,113.6 M499.2,113.6 L499.2,113.5 L499.3,113.5 M499.3,64.8 M499.3,113.5
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- M240.8,182.9 L240.8,183.0 M240.7,182.9 M240.6,182.9 L240.7,182.9 M240.6,182.8 M240.5,182.8 L240.6,182.8 M240.5,182.8 M240.5,182.7
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- M239.6,182.0 L239.6,182.1 M239.6,182.0 M239.5,182.0 L239.6,182.0 M239.5,182.0 M239.5,181.9 M239.4,181.9 L239.5,181.9 M239.4,181.9
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- M237.3,180.2 L237.3,180.3 M237.3,180.2 M237.2,180.2 L237.3,180.2 M237.2,180.2 M237.1,180.1 L237.2,180.1 M237.1,180.1 M237.0,180.0
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- L234.6,178.1 M234.5,178.0 L234.5,178.1 M234.5,178.0 M234.4,178.0 L234.5,178.0 M234.4,178.0 M234.3,177.9 M234.2,177.9 L234.3,177.9
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projects / biopieces.git / commitdiff
