+++ /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: Find the maximum value in the stream for given keys.
-
-Usage: ... | $script [options]
-
-Options: [-k <string> | --keys=<string>] - Comma separated list of keys to inspect.
-Options: [-I <file> | --stream_in=<file>] - Read input stream from file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output stream to file - Default=STDOUT
-
-Examples: ... | $script -k SEQ_LEN - Find the maximum SEQ_LEN.
-
-Keys out: <key>_MAX - Maximum value of <key>.
+++ /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: Calculate the mean of values of given keys.
-
-Usage: ... | $script [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-o <file> | --data_out=<file>] - Write result to file.
-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: ... | $script -x -k SEQ_LEN,HIT_LEN -o result.txt - Calculate mean values and save to 'result.txt'.
-
-Keys out: <key>_MEAN - Mean value of <key>.
-
+++ /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 median values of given keys.
-
-Usage: ... | $script [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-o <file> | --data_out=<file>] - Write result to file.
-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: ... | $script -x -k SEQ_LEN,HIT_LEN -o result.txt - Calculate median values and save to 'result.txt'.
-
-Keys out: <key>_MEDIAN - Median value of <key>.
-
+++ /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: Merge values of keys in a record so that all values are joined with a delimiter and saved as value of the first key.
-
-Usage: ... | $script [options]
-
-Options: [-k <string> | --keys=<string>] - List of values to merge.
-Options: [-d <string> | --delimit=<string>] - Merge delimiter - 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 -k SEQ_NAME,CHR,CHR_BEG,CHR_END - Merges specified values and saves in SEQ_NAME.
-
+++ /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: Find the minimum value in the stream for given keys.
-
-Usage: ... | $script [options]
-
-Options: [-k <string> | --keys=<string>] - Comma separated list of keys to inspect.
-Options: [-I <file> | --stream_in=<file>] - Read input stream from file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output stream to file - Default=STDOUT
-
-Examples: ... | $script -k SEQ_LEN - Find the minimum SEQ_LEN.
-
-Keys out: <key>_MIN - Minimum value of <key>.
+++ /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 total oligo frequencies of sequences in stream.
-
-Usage: ... | oligo_freq [options]
-
-Options: [-w <int> | --word_size=<int>] - Size of oligos - Default=7.
-Options: [-a | --all] - Accumulate oligos for all sequences in stream.
-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: ... | oligo_freq -w 5 - Determines oligo frequency for all sequences in stream.
-Examples: ... | oligo_freq -w 5 -a - Determines accumulated oligo frequency for all sequences in 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: Scan sequences in stream or genomes for patterns using scan_for_matches.
-
-Usage: ... | $script [options]
-Usage: $script [options] -g <genome>
-
-Options: [-p <string> | --patterns=<string>] - Comma separated list of patterns to scan for.
-Options: [-P <file> | --patterns_in=<file>] - File with one pattern per line.
-Options: [-c | --comp] - Scan complementary strand as well.
-Options: [-h <int> | --max_hits=<int>] - Stop scanning after max hits.
-Options: [-m <int> | --max_misses=<int>] - Stop scanning after max misses.
-Options: [-g <genome> | --genome=<genome> - Scan genome for pattern(s).]
-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 -p AATTAA,ATTTAA - Scan sequences in stream for given patterns.
-Examples: $script -g hg18 -P file.pat - Scan hg18 for patterns in 'file.pat'.
+++ /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: Plot chromosome distribution of hits from e.g. BLAT or Vmatch.
-
-Usage: ... | plot_chrdist [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-o <file> | --data_out=<file>] - Write result to file.
-Options: [-t <string> | --terminal=<string>] - Terminal for output: dumb|post|svg - Default=dumb
-Options: [-T <string> | --title=<string>] - Set plot title.
-Options: [-X <string> | --xlabel=<string>] - Set x-axis label.
-Options: [-Y <string> | --ylabel=<string>] - Set y-axis label.
-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: ... | plot_chrdist -x - Create plot and output to STDOUT in ASCII.
-Examples: ... | plot_chrdist -x -t svg -o plot.svg - Create plot and save to 'plot.svg'.
+++ /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: Plot generic histogram.
-
-Usage: ... | plot_histogram [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-o <file> | --data_out=<file>] - Write result to file.
-Options: [-k <string> | --key=<string>] - Key to use for plotting.
-Options: [-t <string> | --terminal=<string>] - Terminal for output: dumb|post|svg - Default=dumb
-Options: [-T <string> | --title=<string>] - Set plot title.
-Options: [-X <string> | --xlabel=<string>] - Set x-axis label.
-Options: [-Y <string> | --ylabel=<string>] - Set y-axis label.
-Options: [-s <num|alph> | --sort=<num|alph>] - Sort criteria for x-axis keys - Default=num
-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: ... | plot_histogram -x -k TISSUE - Create plot and output to STDOUT in ASCII.
-Examples: ... | plot_histogram -x -k TISSUE -t svg -o plot.svg - Create plot and save to 'plot.svg'.
-
+++ /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: Plot hits on a karyogram for a given genome.
-
-Usage: ... | plot_karyogram [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-o <file> | --data_out=<file>] - Write result to file.
-Options: [-g <genome> | --genome=<genome>] - Genome layout of karyogram - Default=hg18
-Options: [-f <string> | --feat_color=<string>] - Color of features - Default=black
-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: ... | plot_karyogram -x -g mm8 -o plot.svg - Create plot and save to 'plot.svg'.
-
+++ /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: Plot length distribution.
-
-Usage: ... | plot_lendist [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-o <file> | --data_out=<file>] - Write result to file.
-Options: [-k <string> | --key=<string>] - Key to use for plotting.
-Options: [-t <string> | --terminal=<string>] - Terminal for output: dumb|post|svg - Default=dumb
-Options: [-T <string> | --title=<string>] - Set plot title.
-Options: [-X <string> | --xlabel=<string>] - Set x-axis label.
-Options: [-Y <string> | --ylabel=<string>] - Set y-axis label.
-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: ... | plot_lendist -x -k HIT_LEN - Create plot and output to STDOUT in ASCII.
-Examples: ... | plot_lendist -x -k HIT_LEN -t svg -o plot.svg - Create plot and save to 'plot.svg'.
+++ /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: Generate a dotplot of matches in stream.
-
-Usage: ... | plot_matches [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-o <file> | --data_out=<file>] - Write result to file.
-Options: [-t <string> | --terminal=<string> - Terminal for output: dumb|post|svg - Default=dumb
-Options: [-d <string> | --direction=<string> - Direction of matches to plot: both|forward|reverse - Default=both
-Options: [-T <string> | --title=<string>] - Set plot title.
-Options: [-X <string> | --xlabel=<string>] - Set x-axis label.
-Options: [-Y <string> | --ylabel=<string>] - Set y-axis label.
-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: ... | plot_matches -x -d forward -t svg -o plot.svg - Create plot and save to 'plot.svg'.
-
+++ /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: Generate a plot of PhastCons profiles based on chromosome coordinates in stream.
-
-Usage: ... | plot_phastcons_profiles [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-o <file> | --data_out=<file>] - Write result to file.
-Options: [-g <genome> | --genome=<genome>] - Genome from which to obtain PhastCons info.
-Options: [-m | --mean] - Calculate a mean profile.
-Options: [-M | --median] - Calculate a median profile.
-Options: [-f <int> | --flank=<int>] - Include flanking PhastCons scores.
-Options: [-t <string> | --terminal=<string> - Terminal for output: dumb|post|svg - Default=dumb
-Options: [-d <string> | --direction=<string> - Direction of matches to plot: both|forward|reverse - Default=both
-Options: [-T <string> | --title=<string>] - Set plot title.
-Options: [-X <string> | --xlabel=<string>] - Set x-axis label.
-Options: [-Y <string> | --ylabel=<string>] - Set y-axis label.
-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: ... | plot_phastcons_profiles -x -g dm3 -f 50 - Create plot of all profiles including 50 flanking scores.
-Examples: ... | plot_phastcons_profiles -x -g dm3 -f 50 -m - Create a mean plot of all profiles including 50 flanking 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: Renders a sequence logo in SVG format from alignment in stream.
-
-Usage: ... | plot_seqlogo [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 stream file - Default=STDOUT
-
-Examples: ... | plot_seqlogo -x -o logo.svg - Create plot and save to 'plot.svg'.
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: December 2007
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Select a number of random records from the stream.
-
-Usage: ... | random_records [options]
-
-Options: [-n <int> | --num=<int>] - Number of random records to select - 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: ... | random_records -n 100 - Output 100 random records to stream.
-
+++ /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: Read sequence entries from one or more files 2bit files. The length of each sequence is also determined.
-
-Usage: $script [options] -i <FASTA file(s)>
-
-Options: [-i <file(s)> | --data_in=<file(s)>] - Comma separated list of files or glob expression to read.
-Options: [-n <int> | --num=<int>] - Limit number of records to read.
-Options: [-N | --no_mask] - Ignore soft masking.
-Options: [-I <file> | --stream_in=<file>] - Read input stream from file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output stream to file - Default=STDOUT
-
-Examples: $script -i test.2bit - Read FASTA entries from file.
-Examples: $script -i test1.2bit,test2.2bit - Read FASTA entries from files.
-Examples: $script -i '*.2bit' - Read FASTA entries from files.
-Examples: $script -i test.2bit -n 10 - Read first 10 entries from file.
-
-Keys out: SEQ_NAME - Name of sequence.
-Keys out: SEQ - Sequence.
-Keys out: SEQ_LEN - Length of sequence.
+++ /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: Read aligned FASTA entries from one or more files. The aligned sequence length is also determined.
-
-Usage: $script [options] -i <FASTA file(s)>
-
-Options: [-i <file(s)> | --data_in=<file(s)>] - Comma separated list of files to read.
-Options: [-n <int> | --num=<int>] - Limit number of records to read.
-Options: [-I <file> | --stream_in=<file>] - Read input stream from file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output stream to file - Default=STDOUT
-
-Examples: $script -i test.fna - Read aligned FASTA entries from file.
-Examples: $script -i test1.fna,test2,fna - Read aligned FASTA entries from files.
-Examples: $script -i '*.fna' - Read aligned FASTA entries from files.
-Examples: $script -i test.fna -n 10 - Read first 10 aligned FASTA entries from file.
-
-Keys out: SEQ_NAME - Name of sequence.
-Keys out: SEQ - Sequence.
-Keys out: ALIGN_LEN - Length of 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: Read tabular BLAST output (-m 8 and -m 9).
-
-Usage: $script [options] -i <BLAST tabular file(s)>
-
-Options: [-i <file(s)> | --data_in=<file(s)>] - Read input data from file.
-Options: [-n <int> | --num=<int>] - Limit number of records to read.
-Options: [-I <file> | --stream_in=<file>] - Read input stream from file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output stream to file - Default=STDOUT
-
-Examples: $script --data_in=test.blast
-
-Keys out: Q_ID - Query ID.
-Keys out: S_ID - Subject ID.
-Keys out: IDENT - Identity (%).
-Keys out: ALIGN_LEN - Alignment length.
-Keys out: MISMATCHES - Number of mismatches.
-Keys out: GAPS - Number of gaps.
-Keys out: Q_BEG - Query begin.
-Keys out: Q_END - Query end.
-Keys out: S_BEG - Subject begin.
-Keys out: S_END - Subject end.
-Keys out: E_VAL - Expect value.
-Keys out: BIT_SCORE - Bit score.
-Keys out: STRAND - Strand.
-Keys out: REC_TYPE - Record type.
+++ /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: Read data in EMBL format.
-
-Usage: $script [options] -i <EMBL file(s)>
-
-Options: [-i <file(s)> | --data_in=<file>] - Read input data from file.
-Options: [-n <int> | --num=<int>] - Limit number of records to read.
-Options: [-k <string> | --keys=<string>] - Match a subset of record keys only.
-Options: [-f <string> | --feats=<string>] - Match a subset of features only.
-Options: [-q <string> | --quals=<string>] - Match a subset of qualifiers only.
-Options: [-I <file> | --stream_in=<file>] - Read input stream from file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output stream to file - Default=STDOUT
-
-Examples: $script -i embl.dat - Read keys, features, and qualifiers.
-Examples: $script -i embl.dat -k AC,DE - Read only Accession number and Description.
-Examples: $script -i embl.dat -k FT,SEQ -f CDS - Read subset of features matching CDS.
-Examples: $script -i embl.dat -k FT,SEQ -f CDS -q gene - Read subset of qualifiers matching gene.
+++ /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: Read Generic Feature Format (GFF v.3) from one or more files.
-
-Usage: $script [options] -i <GFF file(s)>
-
-Options: [-i <file(s)> | --data_in=<file(s)>] - Comma separated list of files or glob expression to read.
-Options: [-n <int> | --num=<int>] - Limit number of records to read.
-Options: [-I <file> | --stream_in=<file>] - Read input stream from file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output stream to file - Default=STDOUT
-
-Examples: $script -i test.gff - Read GFF entries from file.
-
-Keys out:
-
-Keys out: Q_ID - Feature ID.
-Keys out: SOURCE - Feature source.
-Keys out: TYPE - Feature type.
-Keys out: Q_BEG - Begin position
-Keys out: Q_END - End position
-Keys out: SCORE - Score.
-Keys out: STRAND - Strand.
-Keys out: PHASE - Phase.
-Keys out: ATT - Attributes.
-Keys out: ATT_<key> - Breakdown of Attributes into key/value pairs
+++ /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: Read records from a MySQL query.
-
-Usage: $script [options]
-
-Options: [-d <string> | --database=<string>] - MySQL database.
-Options: [-q <string> | --query=<string>] - MySQL query.
-Options: [-u <string> | --user=<string>] - MySQL user name - Default=<fetched from .hg.conf>
-Options: [-p <string> | --password=<string>] - MySQL password - Default=<fetched from .hg.conf>
-Options: [-I <file> | --stream_in=<file>] - Read input stream from file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output stream to file - Default=STDOUT
-
-Examples: $script -d dm3 -q 'SHOW TABLES' - Retreive table information from database.
-Examples: $script -d dm3 -q 'SELECT * FROM estOrientInfo' - Retreive entire estOreintInfo.
-Examples: $script -d dm3 -q 'SELECT * FROM table WHERE Score < 100' - Retreive selected lines from table.
-
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: December 2007
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: Read data in PhastCons format which are included in the stream as BED records.
-
-Usage: $script [options] -i <PhastCons file(s)>
-
-Options: [-i <file(s)> | --data_in=<file(s)>] - Read input data from file.
-Options: [-n <int> | --num=<int>] - Limit number of records to read and output.
-Options: [-m <int> | --min=<int>] - Minimum length of a conserved block - Default=10
-Options: [-d <int> | --dist=<int>] - Maximum distance between conserved blocks - Default=25
-Options: [-t <float> | --threshold=<int>] - Threshold for conserved block - Default=0.8
-Options: [-g <int> | --gap=<int>] - Allow micro-gap in a conserved block - Default=5
-Options: [-I <file> | --stream_in=<file>] - Read input stream from file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output stream to file - Default=STDOUT
-
-Examples: $script -i chr4.pp
-
-Keys out: CHR - Chromosome name.
-Keys out: CHR_BEG - Chromosome begin position.
-Keys out: CHR_END - Chromoeoms end position.
-Keys out: Q_ID - Query ID (feature name).
-Keys out: SCORE - Score.
-Keys out: STRAND - Strand.
-Keys out: THICK_BEG - The starting position at which the feature is drawn thickly.
-Keys out: THICK_END - The ending position at which the feature is drawn thickly.
-Keys out: ITEMRGB - An RGB value of the form R,G,B (e.g. 255,0,0).
-Keys out: BLOCKCOUNT - The number of blocks (exons) in the BED entry.
-Keys out: BLOCKSIZES - A comma separated list of the block sizes.
-Keys out: Q_BEGS - A comma separated list of block starts.
-Keys out: REC_TYPE - Record type.
-Keys out: BED_LEN - Length of BED entry.
-Keys out: BED_COLS - Number of columns in BED line.
+++ /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: Read PSL data (BLAT's default output).
-
-Usage: $script [options] -i <PSL file(s)>
-
-Options: [-i <file(s)> | --data_in=<file(s)>] - Read PSL data from file.
-Options: [-n <int> | --num=<int>] - Limit number of records to read.
-Options: [-I <file> | --stream_in=<file>] - Read input stream from file - Default=STDIN
-Options: [-O <file> | --stream_out=<file>] - Write output stream to file - Default=STDOUT
-
-Examples: $script -i test1.psl,test2.psl
-Examples: $script -i '*.psl'
-
-Keys out: MATCHES - Number of non-repeat matches.
-Keys out: MISMATCHES - Number of mismatches.
-Keys out: REPMATCHES - Number of repeat matches.
-Keys out: NCOUNT - Number of Ns.
-Keys out: QNUMINSERT - Number of inserts in query.
-Keys out: QBASEINSERT - Number of bases inserted in query.
-Keys out: SNUMINSERT - Number of inserts in subject.
-Keys out: SBASEINSERT - Number of bases inserted in subject.
-Keys out: STRAND - Strand.
-Keys out: Q_ID - Query ID.
-Keys out: Q_LEN - Query length.
-Keys out: Q_BEG - Query begin.
-Keys out: Q_END - Query end.
-Keys out: S_ID - Subject ID.
-Keys out: S_LEN - Subject length.
-Keys out: S_BEG - Subject begin.
-Keys out: S_END - Subject end.
-Keys out: BLOCKCOUNT - Block count.
-Keys out: BLOCKSIZES - Block sizes.
-Keys out: Q_BEGS - Query sequence blocks begins.
-Keys out: S_BEGS - Subject sequence blocks begins.
-Keys out: SCORE - Score calculated as in web BLAT results.
-Keys out: REC_TYPE - Record type.
projects / biopieces.git / commitdiff