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<html> <head> <title>MayaChemTools:Documentation:InfoSequenceFiles.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="./InfoSDFiles.html" title="InfoSDFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoTextFiles.html" title="InfoTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>InfoSequenceFiles.pl</strong></td><td width="33%" align="right"><a href="././code/InfoSequenceFiles.html" title="View source code">Code</a> | <a href="./../pdf/InfoSequenceFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/InfoSequenceFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/InfoSequenceFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/InfoSequenceFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> </table> </div> <p> </p> <h2>NAME</h2> <p>InfoSequenceFiles.pl - List information about sequence and alignment files</p> <p> </p> <h2>SYNOPSIS</h2> <p>InfoSequenceFiles.pl SequenceFile(s) AlignmentFile(s)...</p> <p>InfoSequenceFiles.pl [<strong>-a, --all</strong>] [<strong>-c, --count</strong>] [<strong>-d, --detail</strong> infolevel] [<strong>-f, --frequency</strong>] [<strong>--FrequencyBins</strong> number | "number, number, [number,...]"] [<strong>-h, --help</strong>] [<strong>-i, --IgnoreGaps</strong> yes | no] [<strong>-l, --longest</strong>] [<strong>-s, --shortest</strong>] [<strong>--SequenceLengths</strong>] [<strong>-w, --workingdir</strong> dirname] SequenceFile(s)...</p> <p> </p> <h2>DESCRIPTION</h2> <p>List information about contents of <em>SequenceFile(s) and AlignmentFile(s)</em>: number of sequences, shortest and longest sequences, distribution of sequence lengths and so on. 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>-a, --all</strong></strong></dt> <dd> <p>List all the available information.</p> </dd> <dt><strong><strong>-c, --count</strong></strong></dt> <dd> <p>List number of of sequences. This is <strong>default behavior</strong>.</p> </dd> <dt><strong><strong>-d, --detail</strong> <em>InfoLevel</em></strong></dt> <dd> <p>Level of information to print about sequences during various options. Default: <em>1</em>. Possible values: <em>1, 2 or 3</em>.</p> </dd> <dt><strong><strong>-f, --frequency</strong></strong></dt> <dd> <p>List distribution of sequence lengths using the specified number of bins or bin range specified using <strong>FrequencyBins</strong> option.</p> <p>This option is ignored for input files containing only single sequence.</p> </dd> <dt><strong><strong>--FrequencyBins</strong> <em>number | "number,number,[number,...]"</em></strong></dt> <dd> <p>This value is used with <strong>-f, --frequency</strong> option to list distribution of sequence lengths using the specified number of bins or bin range. Default value: <em>10</em>.</p> <p>The bin range list is used to group sequence lengths into different groups; It must contain values in ascending order. Examples:</p> <div class="OptionsBox"> 100,200,300,400,500,600 <br/> 200,400,600,800,1000</div> <p>The frequency value calculated for a specific bin corresponds to all the sequence lengths which are greater than the previous bin value and less than or equal to the current bin value.</p> </dd> <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 during calculation of sequence lengths. Possible values: <em>yes or no</em>. Default value: <em>no</em>.</p> </dd> <dt><strong><strong>-l, --longest</strong></strong></dt> <dd> <p>List information about longest sequence: ID, sequence and sequence length. This option is ignored for input files containing only single sequence.</p> </dd> <dt><strong><strong>-s, --shortest</strong></strong></dt> <dd> <p>List information about shortest sequence: ID, sequence and sequence length. This option is ignored for input files containing only single sequence.</p> </dd> <dt><strong><strong>--SequenceLengths</strong></strong></dt> <dd> <p>List information about sequence lengths.</p> </dd> <dt><strong><strong>-w, --WorkingDir</strong> <em>dirname</em></strong></dt> <dd> <p>Location of working directory. Default: current directory.</p> </dd> </dl> <p> </p> <h2>EXAMPLES</h2> <p>To count number of sequences in sequence files, type:</p> <div class="ExampleBox"> % InfoSequenceFiles.pl Sample1.fasta <br/>% InfoSequenceFiles.pl Sample1.msf Sample1.aln Sample1.pir <br/>% InfoSequenceFiles.pl *.fasta *.fta *.msf *.pir *.aln</div> <p>To list all available information with maximum level of available detail for a sequence alignment file Sample1.msf, type:</p> <div class="ExampleBox"> % InfoSequenceFiles.pl -a -d 3 Sample1.msf</div> <p>To list sequence length information after ignoring sequence gaps in Sample1.aln file, type:</p> <div class="ExampleBox"> % InfoSequenceFiles.pl --SequenceLengths --IgnoreGaps Yes Sample1.aln</div> <p>To list shortest and longest sequence length information after ignoring sequence gaps in Sample1.aln file, type:</p> <div class="ExampleBox"> % InfoSequenceFiles.pl --longest --shortest --IgnoreGaps Yes Sample1.aln</div> <p>To list distribution of sequence lengths after ignoring sequence gaps in Sample1.aln file and report the frequency distribution into 10 bins, type:</p> <div class="ExampleBox"> % InfoSequenceFiles.pl --frequency --FrequencyBins 10 --IgnoreGaps Yes Sample1.aln</div> <p>To list distribution of sequence lengths after ignoring sequence gaps in Sample1.aln file and report the frequency distribution into specified bin range, type:</p> <div class="ExampleBox"> % InfoSequenceFiles.pl --frequency --FrequencyBins "150,200,250,300,350" --IgnoreGaps Yes Sample1.aln</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="./ExtractFromSequenceFiles.html">ExtractFromSequenceFiles.pl</a>, <a href="./InfoAminoAcids.html">InfoAminoAcids.pl</a>, <a href="./InfoNucleicAcids.html">InfoNucleicAcids.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="./InfoSDFiles.html" title="InfoSDFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoTextFiles.html" title="InfoTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>InfoSequenceFiles.pl</strong></td></tr> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>