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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| -1:000000000000 | 0:73ae111cf86f |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Documentation:InfoSequenceFiles.pl</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <div class="DocNav"> | |
| 14 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 15 <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> | |
| 16 </table> | |
| 17 </div> | |
| 18 <p> | |
| 19 </p> | |
| 20 <h2>NAME</h2> | |
| 21 <p>InfoSequenceFiles.pl - List information about sequence and alignment files</p> | |
| 22 <p> | |
| 23 </p> | |
| 24 <h2>SYNOPSIS</h2> | |
| 25 <p>InfoSequenceFiles.pl SequenceFile(s) AlignmentFile(s)...</p> | |
| 26 <p>InfoSequenceFiles.pl [<strong>-a, --all</strong>] [<strong>-c, --count</strong>] [<strong>-d, --detail</strong> infolevel] | |
| 27 [<strong>-f, --frequency</strong>] [<strong>--FrequencyBins</strong> number | "number, number, [number,...]"] | |
| 28 [<strong>-h, --help</strong>] [<strong>-i, --IgnoreGaps</strong> yes | no] [<strong>-l, --longest</strong>] [<strong>-s, --shortest</strong>] | |
| 29 [<strong>--SequenceLengths</strong>] [<strong>-w, --workingdir</strong> dirname] SequenceFile(s)...</p> | |
| 30 <p> | |
| 31 </p> | |
| 32 <h2>DESCRIPTION</h2> | |
| 33 <p>List information about contents of <em>SequenceFile(s) and AlignmentFile(s)</em>: number of sequences, | |
| 34 shortest and longest sequences, distribution of sequence lengths and so on. The file names are | |
| 35 separated by spaces. All the sequence files in a current directory can be specified by <em>*.aln</em>, | |
| 36 <em>*.msf</em>, <em>*.fasta</em>, <em>*.fta</em>, <em>*.pir</em> or any other supported formats; additionally, <em>DirName</em> | |
| 37 corresponds to all the sequence files in the current directory with any of the supported file | |
| 38 extension: <em>.aln, .msf, .fasta, .fta, and .pir</em>.</p> | |
| 39 <p>Supported sequence formats are: <em>ALN/CLustalW</em>, <em>GCG/MSF</em>, <em>PILEUP/MSF</em>, <em>Pearson/FASTA</em>, | |
| 40 and <em>NBRF/PIR</em>. Instead of using file extensions, file formats are detected by parsing the contents | |
| 41 of <em>SequenceFile(s) and AlignmentFile(s)</em>.</p> | |
| 42 <p> | |
| 43 </p> | |
| 44 <h2>OPTIONS</h2> | |
| 45 <dl> | |
| 46 <dt><strong><strong>-a, --all</strong></strong></dt> | |
| 47 <dd> | |
| 48 <p>List all the available information.</p> | |
| 49 </dd> | |
| 50 <dt><strong><strong>-c, --count</strong></strong></dt> | |
| 51 <dd> | |
| 52 <p>List number of of sequences. This is <strong>default behavior</strong>.</p> | |
| 53 </dd> | |
| 54 <dt><strong><strong>-d, --detail</strong> <em>InfoLevel</em></strong></dt> | |
| 55 <dd> | |
| 56 <p>Level of information to print about sequences during various options. Default: <em>1</em>. | |
| 57 Possible values: <em>1, 2 or 3</em>.</p> | |
| 58 </dd> | |
| 59 <dt><strong><strong>-f, --frequency</strong></strong></dt> | |
| 60 <dd> | |
| 61 <p>List distribution of sequence lengths using the specified number of bins or bin range specified | |
| 62 using <strong>FrequencyBins</strong> option.</p> | |
| 63 <p>This option is ignored for input files containing only single sequence.</p> | |
| 64 </dd> | |
| 65 <dt><strong><strong>--FrequencyBins</strong> <em>number | "number,number,[number,...]"</em></strong></dt> | |
| 66 <dd> | |
| 67 <p>This value is used with <strong>-f, --frequency</strong> option to list distribution of sequence lengths using | |
| 68 the specified number of bins or bin range. Default value: <em>10</em>.</p> | |
| 69 <p>The bin range list is used to group sequence lengths into different groups; It must contain | |
| 70 values in ascending order. Examples:</p> | |
| 71 <div class="OptionsBox"> | |
| 72 100,200,300,400,500,600 | |
| 73 <br/> 200,400,600,800,1000</div> | |
| 74 <p>The frequency value calculated for a specific bin corresponds to all the sequence lengths | |
| 75 which are greater than the previous bin value and less than or equal to the current bin value.</p> | |
| 76 </dd> | |
| 77 <dt><strong><strong>-h, --help</strong></strong></dt> | |
| 78 <dd> | |
| 79 <p>Print this help message.</p> | |
| 80 </dd> | |
| 81 <dt><strong><strong>-i, --IgnoreGaps</strong> <em>yes | no</em></strong></dt> | |
| 82 <dd> | |
| 83 <p>Ignore gaps during calculation of sequence lengths. Possible values: <em>yes or | |
| 84 no</em>. Default value: <em>no</em>.</p> | |
| 85 </dd> | |
| 86 <dt><strong><strong>-l, --longest</strong></strong></dt> | |
| 87 <dd> | |
| 88 <p>List information about longest sequence: ID, sequence and sequence length. This option | |
| 89 is ignored for input files containing only single sequence.</p> | |
| 90 </dd> | |
| 91 <dt><strong><strong>-s, --shortest</strong></strong></dt> | |
| 92 <dd> | |
| 93 <p>List information about shortest sequence: ID, sequence and sequence length. This option | |
| 94 is ignored for input files containing only single sequence.</p> | |
| 95 </dd> | |
| 96 <dt><strong><strong>--SequenceLengths</strong></strong></dt> | |
| 97 <dd> | |
| 98 <p>List information about sequence lengths.</p> | |
| 99 </dd> | |
| 100 <dt><strong><strong>-w, --WorkingDir</strong> <em>dirname</em></strong></dt> | |
| 101 <dd> | |
| 102 <p>Location of working directory. Default: current directory.</p> | |
| 103 </dd> | |
| 104 </dl> | |
| 105 <p> | |
| 106 </p> | |
| 107 <h2>EXAMPLES</h2> | |
| 108 <p>To count number of sequences in sequence files, type:</p> | |
| 109 <div class="ExampleBox"> | |
| 110 % InfoSequenceFiles.pl Sample1.fasta | |
| 111 <br/>% InfoSequenceFiles.pl Sample1.msf Sample1.aln Sample1.pir | |
| 112 <br/>% InfoSequenceFiles.pl *.fasta *.fta *.msf *.pir *.aln</div> | |
| 113 <p>To list all available information with maximum level of available detail for a sequence | |
| 114 alignment file Sample1.msf, type:</p> | |
| 115 <div class="ExampleBox"> | |
| 116 % InfoSequenceFiles.pl -a -d 3 Sample1.msf</div> | |
| 117 <p>To list sequence length information after ignoring sequence gaps in Sample1.aln file, type:</p> | |
| 118 <div class="ExampleBox"> | |
| 119 % InfoSequenceFiles.pl --SequenceLengths --IgnoreGaps Yes | |
| 120 Sample1.aln</div> | |
| 121 <p>To list shortest and longest sequence length information after ignoring sequence | |
| 122 gaps in Sample1.aln file, type:</p> | |
| 123 <div class="ExampleBox"> | |
| 124 % InfoSequenceFiles.pl --longest --shortest --IgnoreGaps Yes | |
| 125 Sample1.aln</div> | |
| 126 <p>To list distribution of sequence lengths after ignoring sequence gaps in Sample1.aln file and | |
| 127 report the frequency distribution into 10 bins, type:</p> | |
| 128 <div class="ExampleBox"> | |
| 129 % InfoSequenceFiles.pl --frequency --FrequencyBins 10 | |
| 130 --IgnoreGaps Yes Sample1.aln</div> | |
| 131 <p>To list distribution of sequence lengths after ignoring sequence gaps in Sample1.aln file and | |
| 132 report the frequency distribution into specified bin range, type:</p> | |
| 133 <div class="ExampleBox"> | |
| 134 % InfoSequenceFiles.pl --frequency --FrequencyBins | |
| 135 "150,200,250,300,350" --IgnoreGaps Yes Sample1.aln</div> | |
| 136 <p> | |
| 137 </p> | |
| 138 <h2>AUTHOR</h2> | |
| 139 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
| 140 <p> | |
| 141 </p> | |
| 142 <h2>SEE ALSO</h2> | |
| 143 <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> | |
| 144 </p> | |
| 145 <p> | |
| 146 </p> | |
| 147 <h2>COPYRIGHT</h2> | |
| 148 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
| 149 <p>This file is part of MayaChemTools.</p> | |
| 150 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 151 the terms of the GNU Lesser General Public License as published by the Free | |
| 152 Software Foundation; either version 3 of the License, or (at your option) | |
| 153 any later version.</p> | |
| 154 <p> </p><p> </p><div class="DocNav"> | |
| 155 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 156 <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> | |
| 157 </table> | |
| 158 </div> | |
| 159 <br /> | |
| 160 <center> | |
| 161 <img src="../../images/h2o2.png"> | |
| 162 </center> | |
| 163 </body> | |
| 164 </html> |