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diff mayachemtools/docs/scripts/man1/ExtractFromSequenceFiles.1 @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/scripts/man1/ExtractFromSequenceFiles.1 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,281 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +ExtractFromSequenceFiles.pl \- Extract data from sequence and alignment files +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +ExtractFromSequenceFiles.pl SequenceFile(s) AlignmentFile(s)... +.PP +ExtractFromSequenceFiles.pl [\fB\-h, \-\-help\fR] [\fB\-i, \-\-IgnoreGaps\fR yes | no] +[\fB\-m, \-\-mode\fR SequenceID | SequenceNum | SequenceNumRange] [\fB\-o, \-\-overwrite\fR] +[\fB\-r, \-\-root\fR rootname] [\fB\-s, \-\-Sequences\fR \*(L"SequenceID, [SequenceID,...]\*(R" | \*(L"SequenceNum, [SequenceNum,...]\*(R" | +\&\*(L"StartingSeqNum, EndingSeqNum\*(R"] [\fB\-\-SequenceIDMatch\fR Exact | Relaxed] +[\fB\-w, \-\-WorkingDir\fR dirname] SequenceFile(s) AlignmentFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Extract specific data from \fISequenceFile(s) and AlignmentFile(s)\fR and generate +\&\s-1FASTA\s0 files. You can extract sequences using sequence IDs or sequence numbers. +.PP +The file names are separated by spaces. All the sequence files in a current directory can +be specified by \fI*.aln\fR, \fI*.msf\fR, \fI*.fasta\fR, \fI*.fta\fR, \fI*.pir\fR or any other supported +formats; additionally, \fIDirName\fR corresponds to all the sequence files in the current directory +with any of the supported file extension: \fI.aln, .msf, .fasta, .fta, and .pir\fR. +.PP +Supported sequence formats are: \fIALN/CLustalW\fR, \fI\s-1GCG/MSF\s0\fR, \fI\s-1PILEUP/MSF\s0\fR, \fIPearson/FASTA\fR, +and \fI\s-1NBRF/PIR\s0\fR. Instead of using file extensions, file formats are detected by parsing the contents +of \fISequenceFile(s) and AlignmentFile(s)\fR. +.SH "OPTIONS" +.IX Header "OPTIONS" +.IP "\fB\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message. +.IP "\fB\-i, \-\-IgnoreGaps\fR \fIyes | no\fR" 4 +.IX Item "-i, --IgnoreGaps yes | no" +Ignore gaps or gap columns during during generation of new sequence or alignment file(s). +Possible values: \fIyes or no\fR. Default value: \fIyes\fR. +.Sp +In order to remove gap columns, length of all the sequence must be same; otherwise, +this option is ignored. +.IP "\fB\-m, \-\-mode\fR \fISequenceID | SequenceNum | SequenceNumRange\fR" 4 +.IX Item "-m, --mode SequenceID | SequenceNum | SequenceNumRange" +Specify how to extract data from sequence files: extract sequences using sequence +IDs or sequence numbers. Possible values: \fISequenceID | SequenceNum +| SequenceNumRange\fR. Default: \fISequenceNum\fR with value of 1. +.Sp +The sequence numbers correspond to position of sequences starting from 1 for first sequence +in \fISequenceFile(s) and AlignmentFile(s)\fR. +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files. +.IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4 +.IX Item "-r, --root rootname" +New sequence file name is generated using the root: <Root><Mode>.<Ext>. Default new file: +<SequenceFileName><Mode>.<Ext>. This option is ignored for multiple input files. +.ie n .IP "\fB\-s, \-\-Sequences\fR \fI""SequenceID,[SequenceID,...]"" | ""SequenceNum,[SequenceNum,...]"" | ""StartingSeqNum,EndingSeqNum""\fR" 4 +.el .IP "\fB\-s, \-\-Sequences\fR \fI``SequenceID,[SequenceID,...]'' | ``SequenceNum,[SequenceNum,...]'' | ``StartingSeqNum,EndingSeqNum''\fR" 4 +.IX Item "-s, --Sequences SequenceID,[SequenceID,...] | SequenceNum,[SequenceNum,...] | StartingSeqNum,EndingSeqNum" +This value is \fB\-m, \-\-mode\fR specific. In general, it's a comma delimites list of sequence IDs or sequence +numbers. +.Sp +For \fISequenceID\fR value of \fB\-m, \-\-mode\fR option, input value format is: \fISequenceID,...\fR. Examples: +.Sp +.Vb 2 +\& ACHE_BOVIN +\& ACHE_BOVIN,ACHE_HUMAN +.Ve +.Sp +For \fISequenceNum\fR value of \fB\-m, \-\-mode\fR option, input value format is: \fISequenceNum,...\fR. Examples: +.Sp +.Vb 2 +\& 2 +\& 1,5 +.Ve +.Sp +For \fISequenceNum\fR value of \fB\-m, \-\-mode\fR option, input value format is: \fIStaringSeqNum,EndingSeqNum\fR. Examples: +.Sp +.Vb 1 +\& 2,4 +.Ve +.IP "\fB\-\-SequenceIDMatch\fR \fIExact | Relaxed\fR" 4 +.IX Item "--SequenceIDMatch Exact | Relaxed" +Sequence IDs matching criterion during \fISequenceID\fR value of \fB\-m, \-\-mode\fR option: match +specified sequence \s-1ID\s0 exactly or as sub string against sequence IDs in the files. Possible +values: \fIExact | Relaxed\fR. Default: \fIRelaxed\fR. Sequence \s-1ID\s0 match is case insenstitive +during both options. +.IP "\fB\-\-SequenceLength\fR \fInumber\fR" 4 +.IX Item "--SequenceLength number" +Maximum sequence length per line in sequence file(s). Default: \fI80\fR. +.IP "\fB\-w \-\-WorkingDir\fR \fItext\fR" 4 +.IX Item "-w --WorkingDir text" +Location of working directory. Default: current directory. +.SH "EXAMPLES" +.IX Header "EXAMPLES" +To extract first sequence from Sample1.fasta sequence file and generate Sample1SequenceNum.fasta +sequence file, type: +.PP +.Vb 1 +\& % ExtractFromSequenceFiles.pl \-o Sample1.fasta +.Ve +.PP +To extract first sequence from Sample1.aln alignment file and generate Sample1SequenceNum.fasta +sequence file without any column gaps, type: +.PP +.Vb 1 +\& % ExtractFromSequenceFiles.pl \-o Sample1.aln +.Ve +.PP +To extract first sequence from Sample1.aln alignment file and generate Sample1SequenceNum.fasta +sequence file with column gaps, type: +.PP +.Vb 1 +\& % ExtractFromSequenceFiles.pl \-\-IgnroreGaps No \-o Sample1.aln +.Ve +.PP +To extract sequence number 1 and 4 from Sample1.fasta sequence file and generate +Sample1SequenceNum.fasta sequence file, type: +.PP +.Vb 2 +\& % ExtractFromSequenceFiles.pl \-o \-m SequenceNum \-\-Sequences 1,4 +\& \-o Sample1.fasta +.Ve +.PP +To extract sequences from sequence number 1 to 4 from Sample1.fasta sequence file and generate +Sample1SequenceNumRange.fasta sequence file, type: +.PP +.Vb 2 +\& % ExtractFromSequenceFiles.pl \-o \-m SequenceNumRange \-\-Sequences +\& 1,4 \-o Sample1.fasta +.Ve +.PP +To extract sequence \s-1ID\s0 \*(L"Q9P993/104\-387\*(R" from sequence from Sample1.fasta sequence file and generate +Sample1SequenceID.fasta sequence file, type: +.PP +.Vb 2 +\& % ExtractFromSequenceFiles.pl \-o \-m SequenceID \-\-Sequences +\& "Q9P993/104\-387" \-\-SequenceIDMatch Exact \-o Sample1.fasta +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +AnalyzeSequenceFilesData.pl, InfoSequenceFiles.pl +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.