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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/InfoSequenceFiles.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,164 @@ +<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>