+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: August 2007
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Align sequences in stream using Muscle.
-
-Usage: ... | $script [options]
-
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to stream file - Default=STDOUT
-
-Examples: ... | $script - Aligns all sequences in stream.
-
-Keys in: SEQ_NAME - name of sequence.
-Keys in: Q_ID - used as sequence name if no SEQ_NAME.
-Keys in: SEQ - unaligned sequence.
-
-Keys out: SEQ_NAME - Name of sequence.
-Keys out: SEQ - Aligned sequence.
-Keys out: ALIGN - Number indicating what alignment this sequence belong to.
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: August 2007
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Analysis BED entries in the stream.
-
-Usage: ... | $script [options]
-
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to file - Default=STDOUT
-
-Examples: ... | $script - Analyzes all BED entries in the stream.
-
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: May 2008
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Analyze sequence tags in the stream from sequence or BED records resulting in a tag length and clone count distribution.
-
-Usage: ... | $script [options]
-
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to file - Default=STDOUT
-
-Examples: ... | $script - Analyzes all entries with SEQ in the stream.
-
-Keys in: Q_ID/SEQ_NAME - Identifier with clone/read count: ID00001_123 (123 is the clone count).
-Keys in: SEQ/BED_LEN - Sequence.
-
-Keys out: TAG_LEN - Length of sequence tags.
-Keys out: TAG_COUNT - Number of tags with a given TAG_LEN.
-Keys out: TAG_CLONES - Total clones or reads for all tags (TAG_COUNT) of TAG_LEN.
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: January 2008
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Determine type, count, min, max, sum and mean for values in stream.
-
-Usage: ... | analyze_vals [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-k <string> | --keys=<string>] - Comma separated list of keys.
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to stream file - Default=STDOUT
-
-Examples: ... | analyze_vals -x - Analyses all values in stream.
-Examples: ... | analyze_vals -x -k CHR_BEG,SCORE - Analyses selected values in stream.
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: September 2007
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: BLAST sequences in stream against a specified database.
-
-Usage: ... | blast_seq [options]
-
-Options: [-d <file> | --database=<file>] - Path to database.
-Options: [-g <genome> | --genome=<dm3|hg18|mm8>] - Choose genome instead of database.
-Options: [-p <program> | --program=<program> - blastn|blastp|tblastn|blastx|tblastx - Default=guessed!
-Options: [-e <float> | --e_val=<float>] - Expectation value - Default=10
-Options: [-f | --filter] - Filter low complexity sequence - Default=OFF
-Options: [-F | --no_filter] - Disable low complexity filter - Default
-Options: [-c <int> | --cpus=<int>] - Number of CPUs to use - Default=1
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to stream file - Default=STDOUT
-
-Examples: ... | blast_seq -d my_database - BLAST sequences in stream against custom database.
-Examples: ... | blast_seq -g hg18 - BLAST sequences in stream against hg18.
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: August 2007
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: BLAT sequences in stream against a specified genome.
-
-Usage: ... | $script [options] -g <genome>
-
-Options: [-g <genome> | --genome=<genome> ] - BLAT against genome.
-Options: [-c | --ooc] - Use overused tile file (faster, but less sensitive).
-Options: [-t <int> | --tile_size=<int>] - Size of match that triggers an alignment - Default=11
-Options: [-s <int> | --step_size=<int>] - Spacing between tiles - Default=tile_size
-Options: [-m <int> | --min_identity=<int>] - Minimum sequence identity in percent - Default=90
-Options: [-M <int> | --min_score=<int>] - Minimum score - Default=0
-Options: [-o <int> | --one_off=<int>] - Allows one mismatch in tile - Default=0
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to stream file - Default=STDOUT
-
-Examples: ... | $script -g hg18 - BLAT sequences in stream against hg18.
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: March 2008
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Calculate the bit score for each position based on an alignment in the stream.
-
-Usage: ... | $script [options]
-
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to stream file - Default=STDOUT
-
-Examples: ... | $script - Output a bitscore for each column in the alignment.
-
-Keys out: V0, V1, V2, Vn - Bit score for each position.
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: May 2008
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Generates an index calculated as the most common di-residue over the sequence length for all sequences in stream. An index higher than 0.4 indicates low complexity sequence.
-
-Usage: ... | $script [options]
-
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to file - Default=STDOUT
-
-Examples: ... | $script - Analyzes all sequences in stream.
-
-Keys out: SEQ_COMPLEXITY - Calculated complexity index.
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: February 2008
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Performs computations on records in stream.
-
-Usage: ... | $script [options]
-
-Options: [-e <string> | --eval=<string>] - Evaluate extression.
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to file - Default=STDOUT
-
-Examples: ... | $script -e 'CHR_BEG = 50' - Set CHR_BEG to 50 in all records.
-Examples: ... | $script -e 'CHR_BEG = CHR_BEG - 50' - Substracts 50 from CHR_BEG in all records.
-Examples: ... | $script -e 'CHR_END = CHR_END + BED_LEN' - Adds BED_LEN to CHR_END in all records.
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: August 2007
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Count sequences in stream.
-
-Usage: ... | count_seq [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-o <file> | --data_out=<file>] - Write result to file.
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to file - Default=STDOUT
-
-Examples: ... | count_seq -x -o count.txt - Output records count to 'count.txt'.
-
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: September 2007
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Create a BLAST database from sequences in stream for use with BLAST.
-
-Usage: ... | create_blast_db [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-d <file> | --database=<file>] - Path and name of database to create.
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to stream file - Default=STDOUT
-
-Examples: ... | create_blast_db -x -d /tmp/fly
-
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: January 2008
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Create a vmatch index using mkvtree from sequences in stream for use with vmatch.
-
-Usage: ... | $script [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-i <file> | --index_name=<dir>] - Directory name to contain index files.
-Options: [-p <int> | --prefix_length=<int>] - Minimum prefix that can be matched - Default=guessed
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to stream file - Default=STDOUT
-
-Examples: ... | $script -x -i /tmp/fly
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: June 2008
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Flip table records so rows becomes columns and visa versa.
-
-Usage: ... | $script [options]
-
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to stream file - Default=STDOUT
-
-Examples: ... | $script - Flip rows and columns.
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: April 2008
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Extract alignment from multiple genome alignment either explicitly or using BED/PSL/BLAST entries in stream.
-
-Usage: $script [options] -g <genome>
-Usage: ... | $script [options] -g <genome>
-
-Options: [-g <genome> | --genome=<genome>] - Genome to get alignment from.
-Options: [-c <string> | --chr=<string>] - Chromosome with requested alignment.
-Options: [-b <int> | --beg=<int>] - Begin position of alignment (first residue=1).
-Options: [-e <int> | --end=<int>] - End position of alignment.
-Options: [-l <int> | --len=<int>] - Length of alignment.
-Options: [-s <int> | --strand=<int>] - Strand - Default=+
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to stream file - Default=STDOUT
-
-Examples: $script -g hg18 -c chr1 -b 1 -e 10 - Get the first 10 nucleotides multiz alignment of human genome chr1.
-Examples: $script -g hg18 -c chr1 -b 1 -l 10 - Get the first 10 nucleotides multiz alignment of human genome chr1.
-Examples: ... | $script -g mm8 -s '-' - Get the reverse complement alignment of mouse BED/PSL/BLAST entries.
-
-Keys in: REC_TYPE - Optional record type (BED, PSL, or BLAST).
-Keys in: CHR - Chromosome (for use with BED record type).
-Keys in: CHR_BEG - Chromosome begin.
-Keys in: CHR_END - Chromosome end.
-Keys in: S_ID - Chromosome (for use with PSL and BLAST record type).
-Keys in: S_BEG - Chromosome begin (for use with PSL and BLAST record type).
-Keys in: S_END - Chromosome end (for use with PSL and BLAST record type).
-Keys in: STRAND - Sequence strand.
-
-Keys out: ALIGN - Alignment number that this entry belongs to.
-Keys out: CHR - Chromosome.
-Keys out: CHR_BEG - Chromosome begin.
-Keys out: CHR_END - Chromosome end.
-Keys out: STRAND - Strand.
-Keys out: SEQ - Sequence.
-Keys out: ALIGN_LEN - Sequence length.
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: February 2009
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Extract phastcons scores from a genome either explicitly or using BED/PSL/BLAST entries in stream.
-
-Usage: $script [options] -g <genome>
-Usage: ... | $script [options] -g <genome>
-
-Options: [-g <genome> | --genome=<genome>] - Genome to get phastcons scores from.
-Options: [-c <string> | --chr=<string>] - Chromosome with requested scores.
-Options: [-b <int> | --beg=<int>] - Begin position of interval (first residue=1).
-Options: [-e <int> | --end=<int>] - End position of interval.
-Options: [-l <int> | --len=<int>] - Length of interval.
-Options: [-f <int> | --flank=<int>] - Include flanking region.
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to stream file - Default=STDOUT
-
-Examples: $script -g hg18 -c chr1 -b 1 -e 10 - Get the first 10 phastcons scores from human genome chr1.
-Examples: $script -g hg18 -c chr1 -b 1 -l 10 - Get the first 10 phastcons scores from human genome chr1.
-Examples: ... | $script -g mm8 -f 50 - Get phastcons scores including 50nt flanks of mouse BED/PSL/BLAST entries.
-
-Keys in: REC_TYPE - Optional record type (BED, PSL, or BLAST).
-Keys in: CHR - Chromosome (for use with BED record type).
-Keys in: CHR_BEG - Chromosome begin.
-Keys in: CHR_END - Chromosome end.
-Keys in: S_ID - Chromosome (for use with PSL and BLAST record type).
-Keys in: S_BEG - Chromosome begin (for use with PSL and BLAST record type).
-Keys in: S_END - Chromosome end (for use with PSL and BLAST record type).
-
-Keys out: CHR - Chromosome.
-Keys out: CHR_BEG - Chromosome begin.
-Keys out: CHR_END - Chromosome end.
-Keys out: PHASTCONS - Comma separated list of phastcons scores.
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: August 2007
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Emit the first records in stream.
-
-Usage: ... | head_records
-
-Options: [-n <int> | --num=<int>] - Number of records to emit - Default=10
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to stream file - Default=STDOUT
-
-Examples: ... | head_records -n 40 - Emit the 40 first records from the stream.
-
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: August 2007
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Determines the length of each sequence in stream - and a total length.
-
-Usage: ... | length_seq [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-o <file> | --data_out=<file>] - Write result to file.
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to file - Default=STDOUT
-
-Examples: ... | length_seq -x -o length.txt - Output total length to 'length.txt'.
-
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: August 2007
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Determine the length of the value for given keys.
-
-Usage: ... | length_vals [options]
-
-Options: [-k <string> | --keys=<string>] - Comma separated list of keys.
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to stream file - Default=STDOUT
-
-Examples: ... | length_vals -k SEQ - Determine the length of all SEQ values.
-Examples: ... | length_vals -k HIT,PATTERN - Determine the length of all HIT and PATTERN values.
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: January 2008
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: List the description of all biotools.
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: August 2007
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Find all matches between the first two sequences in stream - or all self-self matches if only one sequence is found.
-
-Usage: ... | match_seq [options]
-
-Options: [-w <int> | --word_size=<int>] - Minimum match size - Default=20
-Options: [-d <string> | --direction=<string>] - Match direction: both|forward|reverse - Default=both
-Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output to stream file - Default=STDOUT
-
-Examples: ... | match_seq -w 25 -d forward
-
projects / biopieces.git / commitdiff