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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/html/ExtractFromSequenceFiles.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,165 @@ +<html> +<head> +<title>MayaChemTools:Documentation:ExtractFromSequenceFiles.pl</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtractFromSDFiles.html" title="ExtractFromSDFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtractFromTextFiles.html" title="ExtractFromTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>ExtractFromSequenceFiles.pl</strong></td><td width="33%" align="right"><a href="././code/ExtractFromSequenceFiles.html" title="View source code">Code</a> | <a href="./../pdf/ExtractFromSequenceFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ExtractFromSequenceFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ExtractFromSequenceFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ExtractFromSequenceFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>ExtractFromSequenceFiles.pl - Extract data from sequence and alignment files</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>ExtractFromSequenceFiles.pl SequenceFile(s) AlignmentFile(s)...</p> +<p>ExtractFromSequenceFiles.pl [<strong>-h, --help</strong>] [<strong>-i, --IgnoreGaps</strong> yes | no] +[<strong>-m, --mode</strong> SequenceID | SequenceNum | SequenceNumRange] [<strong>-o, --overwrite</strong>] +[<strong>-r, --root</strong> rootname] [<strong>-s, --Sequences</strong> "SequenceID, [SequenceID,...]" | "SequenceNum, [SequenceNum,...]" | +"StartingSeqNum, EndingSeqNum"] [<strong>--SequenceIDMatch</strong> Exact | Relaxed] +[<strong>-w, --WorkingDir</strong> dirname] SequenceFile(s) AlignmentFile(s)...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>Extract specific data from <em>SequenceFile(s) and AlignmentFile(s)</em> and generate +FASTA files. You can extract sequences using sequence IDs or sequence numbers.</p> +<p>The file names are separated by spaces. All the sequence files in a current directory can +be specified by <em>*.aln</em>, <em>*.msf</em>, <em>*.fasta</em>, <em>*.fta</em>, <em>*.pir</em> or any other supported +formats; additionally, <em>DirName</em> corresponds to all the sequence files in the current directory +with any of the supported file extension: <em>.aln, .msf, .fasta, .fta, and .pir</em>.</p> +<p>Supported sequence formats are: <em>ALN/CLustalW</em>, <em>GCG/MSF</em>, <em>PILEUP/MSF</em>, <em>Pearson/FASTA</em>, +and <em>NBRF/PIR</em>. Instead of using file extensions, file formats are detected by parsing the contents +of <em>SequenceFile(s) and AlignmentFile(s)</em>.</p> +<p> +</p> +<h2>OPTIONS</h2> +<dl> +<dt><strong><strong>-h, --help</strong></strong></dt> +<dd> +<p>Print this help message.</p> +</dd> +<dt><strong><strong>-i, --IgnoreGaps</strong> <em>yes | no</em></strong></dt> +<dd> +<p>Ignore gaps or gap columns during during generation of new sequence or alignment file(s). +Possible values: <em>yes or no</em>. Default value: <em>yes</em>.</p> +<p>In order to remove gap columns, length of all the sequence must be same; otherwise, +this option is ignored.</p> +</dd> +<dt><strong><strong>-m, --mode</strong> <em>SequenceID | SequenceNum | SequenceNumRange</em></strong></dt> +<dd> +<p>Specify how to extract data from sequence files: extract sequences using sequence +IDs or sequence numbers. Possible values: <em>SequenceID | SequenceNum +| SequenceNumRange</em>. Default: <em>SequenceNum</em> with value of 1.</p> +<p>The sequence numbers correspond to position of sequences starting from 1 for first sequence +in <em>SequenceFile(s) and AlignmentFile(s)</em>.</p> +</dd> +<dt><strong><strong>-o, --overwrite</strong></strong></dt> +<dd> +<p>Overwrite existing files.</p> +</dd> +<dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> +<dd> +<p>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.</p> +</dd> +<dt><strong><strong>-s, --Sequences</strong> <em>"SequenceID,[SequenceID,...]" | "SequenceNum,[SequenceNum,...]" | "StartingSeqNum,EndingSeqNum"</em></strong></dt> +<dd> +<p>This value is <strong>-m, --mode</strong> specific. In general, it's a comma delimites list of sequence IDs or sequence +numbers.</p> +<p>For <em>SequenceID</em> value of <strong>-m, --mode</strong> option, input value format is: <em>SequenceID,...</em>. Examples:</p> +<div class="OptionsBox"> + ACHE_BOVIN +<br/> ACHE_BOVIN,ACHE_HUMAN</div> +<p>For <em>SequenceNum</em> value of <strong>-m, --mode</strong> option, input value format is: <em>SequenceNum,...</em>. Examples:</p> +<div class="OptionsBox"> + 2 +<br/> 1,5</div> +<p>For <em>SequenceNum</em> value of <strong>-m, --mode</strong> option, input value format is: <em>StaringSeqNum,EndingSeqNum</em>. Examples:</p> +<div class="OptionsBox"> + 2,4</div> +</dd> +<dt><strong><strong>--SequenceIDMatch</strong> <em>Exact | Relaxed</em></strong></dt> +<dd> +<p>Sequence IDs matching criterion during <em>SequenceID</em> value of <strong>-m, --mode</strong> option: match +specified sequence ID exactly or as sub string against sequence IDs in the files. Possible +values: <em>Exact | Relaxed</em>. Default: <em>Relaxed</em>. Sequence ID match is case insenstitive +during both options.</p> +</dd> +<dt><strong><strong>--SequenceLength</strong> <em>number</em></strong></dt> +<dd> +<p>Maximum sequence length per line in sequence file(s). Default: <em>80</em>.</p> +</dd> +<dt><strong><strong>-w --WorkingDir</strong> <em>text</em></strong></dt> +<dd> +<p>Location of working directory. Default: current directory.</p> +</dd> +</dl> +<p> +</p> +<h2>EXAMPLES</h2> +<p>To extract first sequence from Sample1.fasta sequence file and generate Sample1SequenceNum.fasta +sequence file, type:</p> +<div class="ExampleBox"> + % ExtractFromSequenceFiles.pl -o Sample1.fasta</div> +<p>To extract first sequence from Sample1.aln alignment file and generate Sample1SequenceNum.fasta +sequence file without any column gaps, type:</p> +<div class="ExampleBox"> + % ExtractFromSequenceFiles.pl -o Sample1.aln</div> +<p>To extract first sequence from Sample1.aln alignment file and generate Sample1SequenceNum.fasta +sequence file with column gaps, type:</p> +<div class="ExampleBox"> + % ExtractFromSequenceFiles.pl --IgnroreGaps No -o Sample1.aln</div> +<p>To extract sequence number 1 and 4 from Sample1.fasta sequence file and generate +Sample1SequenceNum.fasta sequence file, type:</p> +<div class="ExampleBox"> + % ExtractFromSequenceFiles.pl -o -m SequenceNum --Sequences 1,4 + -o Sample1.fasta</div> +<p>To extract sequences from sequence number 1 to 4 from Sample1.fasta sequence file and generate +Sample1SequenceNumRange.fasta sequence file, type:</p> +<div class="ExampleBox"> + % ExtractFromSequenceFiles.pl -o -m SequenceNumRange --Sequences + 1,4 -o Sample1.fasta</div> +<p>To extract sequence ID "Q9P993/104-387" from sequence from Sample1.fasta sequence file and generate +Sample1SequenceID.fasta sequence file, type:</p> +<div class="ExampleBox"> + % ExtractFromSequenceFiles.pl -o -m SequenceID --Sequences + "Q9P993/104-387" --SequenceIDMatch Exact -o Sample1.fasta</div> +<p> +</p> +<h2>AUTHOR</h2> +<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> +<p> +</p> +<h2>SEE ALSO</h2> +<p><a href="./AnalyzeSequenceFilesData.html">AnalyzeSequenceFilesData.pl</a>, <a href="./InfoSequenceFiles.html">InfoSequenceFiles.pl</a> +</p> +<p> +</p> +<h2>COPYRIGHT</h2> +<p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> +<p>This file is part of MayaChemTools.</p> +<p>MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.</p> +<p> </p><p> </p><div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtractFromSDFiles.html" title="ExtractFromSDFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtractFromTextFiles.html" title="ExtractFromTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ExtractFromSequenceFiles.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>