+++ /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: Read data in GEO soft format. NCBI's deep sequencing and micro array data format.
-
-Usage: $script [options] -i <soft 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: [-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 GSE6734_family.soft
-
-Keys out: SAMPLE_TITLE - Title of sample.
-Keys out: SEQ_NAME - Sequence name composed of Platform Series ID, Sample GEO accession, Sequence number in current experiment, and read count.
-Keys out: SEQ - Sequence.
+++ /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: Read Solexa deep sequenceing output files. Lowercase sequence indicates low quality.
-
-Usage: $script [options] -i <Solexa 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: [-q <int> | --quality=<int>] - Lowercase nucleotide with quality score below this limit (min:0 max:40) - Default=20
-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.solexa - Read Solexa entries from file.
-Examples: $script -i test1.fna,test2.solexa - Read Solexa entries from files.
-Examples: $script -i '*.solexa' - Read Solexa entries from files.
-Examples: $script -i test.solexa -n 10 - Read first 10 Solexa entries from file.
-Examples: $script -i test.solexa -q 10 - Change quality score threshold to 10.
-
-Keys out: SEQ_NAME - Name of sequence.
-Keys out: SEQ - Sequence.
-Keys out: SEQ_LEN - Length of sequence.
-Keys out: SCORE_MEAN - Mean quality score.
+++ /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: Read Solid sequence files with Name, Sequence and Quality.
-
-Usage: $script [options] -i <Solid 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: [-q <int> | --quality=<int>] - Lowercase nucleotide with quality score below this limit (min:0 max:40) - Default=20
-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.solid - Read Solid entries from file.
-Examples: $script -i test1.fna,test2.solid - Read Solid entries from files.
-Examples: $script -i '*.solid' - Read Solid entries from files.
-Examples: $script -i test.solid -n 10 - Read first 10 Solid entries from file.
-Examples: $script -i test.solid -q 10 - Change quality score threshold to 10.
-
-Keys out: SEQ_NAME - Name of sequence.
-Keys out: SEQ_CS - Sequence in color space.
-Keys out: SEQ_QUAL - Sequence quality.
-Keys out: SEQ - Sequence.
-Keys out: SEQ_LEN - Length of sequence.
-Keys out: SCORE_MEAN - Mean quality score.
+++ /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 Stockholm format.
-
-Usage: $script [options] -i <Stockholm 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 -i test.stockholm
-
-Keys out: SEQ_NAME - Sequence name.
-Keys out: SEQ - Aligned sequence.
-Keys out: ALIGN - Number indicating what alignment this sequence belongs 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: Remove indels (-~.) from sequences in stream.
-
-Usage: ... | remove_indels [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: ... | remove_indels - Removes indels from 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: Remove given keys from records in stream.
-
-Usage: ... | remove_keys [options]
-
-Options: [-k <string> | --keys=<string>] - Comma separeted list of keys to remove.
-Options: [-K <string> | --save_keys=<string>] - Remove all save these comma separeted 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: ... | remove_keys -k 'SEQ_NAME,SEQ' - Removes SEQ_NAME and SEQ from all records in stream.
-Examples: ... | remove_keys -K 'SEQ_NAME,SEQ' - Removes all keys except SEQ_NAME and SEQ.
-
+++ /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: Shuffle sequences in 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 - Shuffles all sequences in stream.
-
-Keys in: SEQ - 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: Split BED records into overlapping windows.
-
-Usage: ... | $script [options]
-
-Options: [-w <int> | --window_size=<int>] - Window size - Default=20
-Options: [-s <int> | --step_size=<int>] - Step size - 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: ... | $script -w 12 - Split BED record into windows of size 12.
-Examples: ... | $script -s 5 - Split BED record usint windows overlapping every 5th nucleotide.
-
-Keys in: CHR - Chromosome.
-Keys in: CHR_BEG - Chromosome begin position.
-Keys in: CHR_END - Chromosome end position.
-
-Keys out: REC_TYPE - Record type (BED).
-Keys out: CHR - Chromosome.
-Keys out: CHR_BEG - Chromosome begin position.
-Keys out: CHR_END - Chromosome end position.
+++ /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: Split sequences in stream into overlapping oligos.
-
-Usage: ... | $script [options]
-
-Options: [-w <int> | --word_size=<int>] - Word size of oligos - Default=7
-Options: [-u | --uniq] - Only emit unique oligos.
-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 -w 12 -u - Only emit uniq oligoes of size 12.
-
-Keys in: SEQ_NAME - Sequence name.
-Keys in: SEQ - 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: Calculate the total sums for the 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 - Sum values and save to 'result.txt'.
-
-Keys out: - <key>_SUM - Sum of 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: Translate DNA sequence into protein sequence.
-
-Usage: ... | $script [options]
-
-Options: [-f <string> | --frames=<string>] - Comma separated list of frames of translation: 1,2,3,-1,-2,-3 - Default=all
-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 -f 1 - Translate into first forward reading frame.
-Examples: ... | $script -f "-1,-2,-3" - Translate into all reverse reading frames.
-
-Keys in: SEQ - Sequence.
-
-Keys out: FRAME - Frame of translation.
+++ /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: Upload data to local UCSC database for viewing in Genome Browser. In order to display secondary structures for folded RNA you must include 'rnaSecStr' in the table name.
-
-Usage: ... | $script [options] <-d <genome>> <-t <string>>
-
-Options: [-d <genome> | --database=<genome>] - Genome database to upload track to.
-Options: [-t <string> | --table=<string>] - Table name of track - NB! prefix with initials. e.g.: mah_test.
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-s <string> | --short_label=<string>] - Short label for track - Default=<table>
-Options: [-l <string> | --long_label=<string>] - Long label for track - Default=<table>
-Options: [-g <string> | --group=<string>] - Track group name - Default=m.hansen
-Options: [-p <float> | --priority=<float>] - Track display priority - Default=1
-Options: [-u | --use_score] - Use the score to grey shade the track.
-Options: [-v <string> | --visibility=<string> - Track visibility: hide|dense|squish|pack|full - Default=pack
-Options: [-w | --wiggle - Create wiggle track based on overlapping sequences.
-Options: [-c <rgb> | --color=<rgb>] - Track color e.g. '147,73,42' - Default=<random>
-Options: [-C <int> | --chunk_size=<int>] - Chunks for loading - Default=10000000
-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 -d hg18 -t initials_my_test
-
+++ /dev/null
-Author: Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact: mail@maasha.dk
-
-Date: October 2007
-
-License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description: vmatch sequences in stream against a specified genome.
-
-Usage: ... | $script [options] -g <genome>
-Usage: ... | $script [options] -i <index>
-
-Options: [-g <genome> | --genome=<genome] - Genome to vmatch.
-Options: [-i <index> | --index_name=<index>] - Custom index to vmatch.
-Options: [-c | --count] - Replace score with hit count.
-Options: [-m | --max_hits] - Skip hits with more than maximum hits (implies --count).
-Options: [-h <string> | --hamming_dist=<string>] - Allow mismatches.
-Options: [-e <string> | --edit_dist=<string>] - Allow mismatches and indels.
-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 - Match sequences in stream againt human genome.
-Examples: ... | $script -g hg18 -h 1 - allowing for one mismatch.
-Examples: ... | $script -g hg18 -h 5p - allowing for 5% mismatches.
-Examples: ... | $script -g hg18 -e 2 - allowing for 2 mismatches or indels.
-Examples: ... | $script -g hg18 -e 10p - allowing for 10% mismatches or indels.
-
+++ /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: Write sequences in 2bit format.
-
-Usage: ... | $script [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-o <file> | --data_out=<file>] - Write result to file.
-Options: [-N | --no_mask] - Ignore soft masking.
-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 -o test.2bit - Write entries to file 'test.2bit'.
-
-Keys in: SEQ_NAME - Sequence name.
-Keys in: Q_ID - Used as sequence name if no SEQ_NAME.
-Keys in: SEQ - 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: Write aligned sequences in pretty alignment format.
-
-Usage: ... | $script [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-o <file> | --data_out=<file>] - Write result to file.
-Options: [-w <int> | --wrap=<int>] - Wrap sequences to a given width.
-Options: [-R | --no_ruler] - Suppress ruler for multiple alignments.
-Options: [-C | --no_consensus] - Suppress consensus for multiple alignments.
-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 -w 80 - Write entries wrapped to blocks of 80 to STDOUT.
-Examples: ... | $script -x -o test.aln - Write entries to file 'test.aln'.
-
-Keys in: SEQ_NAME - Sequence name.
-Keys in: SEQ - Sequence.
-Keys in: ALIGN - Number specifying what alignment the 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: Write BLAST records from stream in BLAST tabular format (-m8 and 9).
-
-Usage: ... | $script [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-o <file> | --data_out=<file>] - Write result to file.
-Options: [-c | --comment] - Print comment line - Default=no
-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
-Options: [-Z | --compress] - Compress output using gzip.
-
-Examples: ... | $script -x -c -o blast.tab - Write BLAST table with comment line to 'blast.tab'.
-Examples: ... | $script -x -Z -o blast.tab.gz - Write zipped BLAST table to 'blast.tab.gz'.
-
-Keys in: Q_ID - Query ID.
-Keys in: S_ID - Subject ID.
-Keys in: IDENT - Identity.
-Keys in: ALIGN_LEN - Alignment length.
-Keys in: MISMATCHES - Mismatches.
-Keys in: GAPS - Gaps.
-Keys in: Q_BEG - Query begin.
-Keys in: Q_END - Query end.
-Keys in: S_BEG - Subject begin.
-Keys in: S_END - Subject end.
-Keys in: E_VAL - Expect value.
-Keys in: BIT_SCORE - Bit score.
-Keys in: STRAND - Strand.
-Keys in: REC_TYPE - Record type must be BLAST.
+++ /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: Write records from stream in PSL format.
-
-Usage: ... | $script [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
-Options: [-Z | --compress] - Compress output using gzip.
-
-Examples: ... | $script -x -o table.psl - Output data to file 'table.psl'.
-Examples: ... | $script -Z -o table.psl.gz - Output zipped data to file 'table.psl.gz'.
-
-Keys in: MATCHES - Number of non-repeat matches.
-Keys in: MISMATCHES - Number of mismatches.
-Keys in: REPMATCHES - Number of repeat matches.
-Keys in: NCOUNT - Number of Ns.
-Keys in: QNUMINSERT - Number of inserts in query.
-Keys in: QBASEINSERT - Number of bases inserted in query.
-Keys in: SNUMINSERT - Number of inserts in subject.
-Keys in: SBASEINSERT - Number of bases inserted in subject.
-Keys in: STRAND - Strand.
-Keys in: Q_ID - Query ID.
-Keys in: Q_LEN - Query length.
-Keys in: Q_BEG - Query begin.
-Keys in: Q_END - Query end.
-Keys in: S_ID - Subject ID.
-Keys in: S_LEN - Subject length.
-Keys in: S_BEG - Subject begin.
-Keys in: S_END - Subject end.
-Keys in: BLOCKCOUNT - Block count.
-Keys in: BLOCKSIZES - Block sizes.
-Keys in: Q_BEGS - Query sequence blocks begins.
-Keys in: S_BEGS - Subject sequence blocks begins.
-Keys in: SCORE - Score calculated as in web BLAT results.
-Keys in: REC_TYPE - Record type.
-
+++ /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: Write di-base encoded Solid sequences.
-
-Usage: ... | $script [options]
-
-Options: [-x | --no_stream] - Do not emit records.
-Options: [-o <file> | --data_out=<file>] - Write result to file.
-Options: [-w <int> | --wrap=<int>] - Wrap sequences to a given width.
-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
-Options: [-Z | --compress] - Compress output using gzip.
-
-Examples: ... | $script -x -w 80 - Write entries wrapped to blocks of 80 to STDOUT.
-Examples: ... | $script -x -o test.solid - Write entries to file 'test.solid'.
-Examples: ... | $script -x -Z -o test.solid.gz - Write zipped entries to file 'test.solid.gz'.
-
-Keys in: SEQ_NAME - Sequence name.
-Keys in: Q_ID - Used as sequence name if no SEQ_NAME.
-Keys in: SEQ - Sequence.
projects / biopieces.git / commitdiff