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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Documentation:AnalyzeSequenceFilesData.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="./AnalyzeSDFilesData.html" title="AnalyzeSDFilesData.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AnalyzeTextFilesData.html" title="AnalyzeTextFilesData.html">Next</a></td><td width="34%" align="middle"><strong>AnalyzeSequenceFilesData.pl</strong></td><td width="33%" align="right"><a href="././code/AnalyzeSequenceFilesData.html" title="View source code">Code</a> | <a href="./../pdf/AnalyzeSequenceFilesData.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/AnalyzeSequenceFilesData.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/AnalyzeSequenceFilesData.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/AnalyzeSequenceFilesData.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>AnalyzeSequenceFilesData.pl - Analyze sequence and alignment files</p> | |
| 22 <p> | |
| 23 </p> | |
| 24 <h2>SYNOPSIS</h2> | |
| 25 <p>AnalyzeSequenceFilesData.pl SequenceFile(s) AlignmentFile(s)...</p> | |
| 26 <p>AnalyzeSequenceFilesData.pl [<strong>-h, --help</strong>] [<strong>-i, --IgnoreGaps</strong> yes | no] | |
| 27 [<strong>-m, --mode</strong> PercentIdentityMatrix | ResidueFrequencyAnalysis | All] | |
| 28 [<strong>--outdelim</strong> comma | tab | semicolon] [<strong>-o, --overwrite</strong>] [<strong>-p, --precision</strong> number] [<strong>-q, --quote</strong> yes | no] | |
| 29 [<strong>--ReferenceSequence</strong> SequenceID | UseFirstSequenceID] | |
| 30 [<strong>--region</strong> "StartResNum, EndResNum, [StartResNum, EndResNum...]" | UseCompleteSequence] | |
| 31 [<strong>--RegionResiduesMode</strong> AminoAcids | NucleicAcids | None] | |
| 32 [<strong>-w, --WorkingDir</strong> dirname] SequenceFile(s) AlignmentFile(s)...</p> | |
| 33 <p> | |
| 34 </p> | |
| 35 <h2>DESCRIPTION</h2> | |
| 36 <p>Analyze <em>SequenceFile(s) and AlignmentFile(s)</em> data: calculate pairwise percent identity matrix or | |
| 37 calculate percent occurrence of various residues in specified sequence regions. All the sequences | |
| 38 in the input file must have the same sequence lengths; otherwise, the sequence file is ignored.</p> | |
| 39 <p>The file names are separated by spaces. All the sequence files in a current directory can | |
| 40 be specified by <em>*.aln</em>, <em>*.msf</em>, <em>*.fasta</em>, <em>*.fta</em>, <em>*.pir</em> or any other supported | |
| 41 formats; additionally, <em>DirName</em> corresponds to all the sequence files in the current directory | |
| 42 with any of the supported file extension: <em>.aln, .msf, .fasta, .fta, and .pir</em>.</p> | |
| 43 <p>Supported sequence formats are: <em>ALN/CLustalW</em>, <em>GCG/MSF</em>, <em>PILEUP/MSF</em>, <em>Pearson/FASTA</em>, | |
| 44 and <em>NBRF/PIR</em>. Instead of using file extensions, file formats are detected by parsing the contents | |
| 45 of <em>SequenceFile(s) and AlignmentFile(s)</em>.</p> | |
| 46 <p> | |
| 47 </p> | |
| 48 <h2>OPTIONS</h2> | |
| 49 <dl> | |
| 50 <dt><strong><strong>-h, --help</strong></strong></dt> | |
| 51 <dd> | |
| 52 <p>Print this help message.</p> | |
| 53 </dd> | |
| 54 <dt><strong><strong>-i, --IgnoreGaps</strong> <em>yes | no</em></strong></dt> | |
| 55 <dd> | |
| 56 <p>Ignore gaps during calculation of sequence lengths and specification of regions during residue | |
| 57 frequency analysis. Possible values: <em>yes or no</em>. Default value: <em>yes</em>.</p> | |
| 58 </dd> | |
| 59 <dt><strong><strong>-m, --mode</strong> <em>PercentIdentityMatrix | ResidueFrequencyAnalysis | All</em></strong></dt> | |
| 60 <dd> | |
| 61 <p>Specify how to analyze data in sequence files: calculate percent identity matrix or calculate | |
| 62 frequency of occurrence of residues in specific regions. During <em>ResidueFrequencyAnalysis</em> value | |
| 63 of <strong>-m, --mode</strong> option, output files are generated for both the residue count and percent residue | |
| 64 count. Possible values: <em>PercentIdentityMatrix, ResidueFrequencyAnalysis, or All</em>. Default value: | |
| 65 <em>PercentIdentityMatrix</em>.</p> | |
| 66 </dd> | |
| 67 <dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt> | |
| 68 <dd> | |
| 69 <p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em>. | |
| 70 Default value: <em>comma</em>.</p> | |
| 71 </dd> | |
| 72 <dt><strong><strong>-o, --overwrite</strong></strong></dt> | |
| 73 <dd> | |
| 74 <p>Overwrite existing files.</p> | |
| 75 </dd> | |
| 76 <dt><strong><strong>-p, --precision</strong> <em>number</em></strong></dt> | |
| 77 <dd> | |
| 78 <p>Precision of calculated values in the output file. Default: up to <em>2</em> decimal places. | |
| 79 Valid values: positive integers.</p> | |
| 80 </dd> | |
| 81 <dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt> | |
| 82 <dd> | |
| 83 <p>Put quotes around column values in output text file. Possible values: <em>yes or | |
| 84 no</em>. Default value: <em>yes</em>.</p> | |
| 85 </dd> | |
| 86 <dt><strong><strong>--ReferenceSequence</strong> <em>SequenceID | UseFirstSequenceID</em></strong></dt> | |
| 87 <dd> | |
| 88 <p>Specify reference sequence ID to identify regions for performing <em>ResidueFrequencyAnalysis</em> specified | |
| 89 using <strong>-m, --mode</strong> option. Default: <em>UseFirstSequenceID</em>.</p> | |
| 90 </dd> | |
| 91 <dt><strong><strong>--region</strong> <em>StartResNum,EndResNum,[StartResNum,EndResNum...] | UseCompleteSequence</em></strong></dt> | |
| 92 <dd> | |
| 93 <p>Specify how to perform frequency of occurrence analysis for residues: use specific regions | |
| 94 indicated by starting and ending residue numbers in reference sequence or use the whole reference | |
| 95 sequence as one region. Default: <em>UseCompleteSequence</em>.</p> | |
| 96 <p>Based on the value of <strong>-i, --IgnoreGaps</strong> option, specified residue numbers <em>StartResNum,EndResNum</em> | |
| 97 correspond to the positions in the reference sequence without gaps or with gaps.</p> | |
| 98 <p>For residue numbers corresponding to the reference sequence including gaps, percent occurrence | |
| 99 of various residues corresponding to gap position in reference sequence is also calculated.</p> | |
| 100 </dd> | |
| 101 <dt><strong><strong>--RegionResiduesMode</strong> <em>AminoAcids | NucleicAcids | None</em></strong></dt> | |
| 102 <dd> | |
| 103 <p>Specify how to process residues in the regions specified using <strong>--region</strong> option during | |
| 104 <em>ResidueFrequencyAnalysis</em> calculation: categorize residues as amino acids, nucleic acids, or simply | |
| 105 ignore residue category during the calculation. Possible values: <em>AminoAcids, NucleicAcids or None</em>. | |
| 106 Default value: <em>None</em>.</p> | |
| 107 <p>For <em>AminoAcids</em> or <em>NucleicAcids</em> values of <strong>--RegionResiduesMode</strong> option, all the standard amino | |
| 108 acids or nucleic acids are listed in the output file for each region; Any gaps and other non standard residues | |
| 109 are added to the list as encountered.</p> | |
| 110 <p>For <em>None</em> value of <strong>--RegionResiduesMode</strong> option, no assumption is made about type of residues. | |
| 111 Residue and gaps are added to the list as encountered.</p> | |
| 112 </dd> | |
| 113 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> | |
| 114 <dd> | |
| 115 <p>New sequence file name is generated using the root: <Root><Mode>.<Ext> and | |
| 116 <Root><Mode><RegionNum>.<Ext>. Default new file | |
| 117 name: <SequenceFileName><Mode>.<Ext> for <em>PercentIdentityMatrix</em> value <strong>m, --mode</strong> option | |
| 118 and <SequenceFileName><Mode><RegionNum>.<Ext> for <em>ResidueFrequencyAnalysis</em>. | |
| 119 The csv, and tsv <Ext> values are used for comma/semicolon, and tab delimited text | |
| 120 files respectively. This option is ignored for multiple input files.</p> | |
| 121 </dd> | |
| 122 <dt><strong><strong>-w --WorkingDir</strong> <em>text</em></strong></dt> | |
| 123 <dd> | |
| 124 <p>Location of working directory. Default: current directory.</p> | |
| 125 </dd> | |
| 126 </dl> | |
| 127 <p> | |
| 128 </p> | |
| 129 <h2>EXAMPLES</h2> | |
| 130 <p>To calculate percent identity matrix for all sequences in Sample1.msf file and generate | |
| 131 Sample1PercentIdentityMatrix.csv, type:</p> | |
| 132 <div class="ExampleBox"> | |
| 133 % AnalyzeSequenceFilesData.pl Sample1.msf</div> | |
| 134 <p>To perform residue frequency analysis for all sequences in Sample1.aln file corresponding to | |
| 135 non-gap positions in the first sequence and generate Sample1ResidueFrequencyAnalysisRegion1.csv | |
| 136 and Sample1PercentResidueFrequencyAnalysisRegion1.csv files, type:</p> | |
| 137 <div class="ExampleBox"> | |
| 138 % AnalyzeSequenceFilesData.pl -m ResidueFrequencyAnalysis -o | |
| 139 Sample1.aln</div> | |
| 140 <p>To perform residue frequency analysis for all sequences in Sample1.aln file corresponding to | |
| 141 all positions in the first sequence and generate TestResidueFrequencyAnalysisRegion1.csv | |
| 142 and TestPercentResidueFrequencyAnalysisRegion1.csv files, type:</p> | |
| 143 <div class="ExampleBox"> | |
| 144 % AnalyzeSequenceFilesData.pl -m ResidueFrequencyAnalysis --IgnoreGaps | |
| 145 No -o -r Test Sample1.aln</div> | |
| 146 <p>To perform residue frequency analysis for all sequences in Sample1.aln file corresponding to | |
| 147 non-gap residue positions 5 to 10, and 30 to 40 in sequence ACHE_BOVIN and generate | |
| 148 Sample1ResidueFrequencyAnalysisRegion1.csv, Sample1ResidueFrequencyAnalysisRegion2.csv, | |
| 149 SamplePercentResidueFrequencyAnalysisRegion1.csv, and | |
| 150 SamplePercentResidueFrequencyAnalysisRegion2.csv files, type:</p> | |
| 151 <div class="ExampleBox"> | |
| 152 % AnalyzeSequenceFilesData.pl -m ResidueFrequencyAnalysis | |
| 153 --ReferenceSequence ACHE_BOVIN --region "5,15,30,40" -o Sample1.msf</div> | |
| 154 <p> | |
| 155 </p> | |
| 156 <h2>AUTHOR</h2> | |
| 157 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
| 158 <p> | |
| 159 </p> | |
| 160 <h2>SEE ALSO</h2> | |
| 161 <p><a href="./ExtractFromSequenceFiles.html">ExtractFromSequenceFiles.pl</a>, <a href="./InfoSequenceFiles.html">InfoSequenceFiles.pl</a> | |
| 162 </p> | |
| 163 <p> | |
| 164 </p> | |
| 165 <h2>COPYRIGHT</h2> | |
| 166 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
| 167 <p>This file is part of MayaChemTools.</p> | |
| 168 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 169 the terms of the GNU Lesser General Public License as published by the Free | |
| 170 Software Foundation; either version 3 of the License, or (at your option) | |
| 171 any later version.</p> | |
| 172 <p> </p><p> </p><div class="DocNav"> | |
| 173 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 174 <tr align="left" valign="top"><td width="33%" align="left"><a href="./AnalyzeSDFilesData.html" title="AnalyzeSDFilesData.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AnalyzeTextFilesData.html" title="AnalyzeTextFilesData.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>AnalyzeSequenceFilesData.pl</strong></td></tr> | |
| 175 </table> | |
| 176 </div> | |
| 177 <br /> | |
| 178 <center> | |
| 179 <img src="../../images/h2o2.png"> | |
| 180 </center> | |
| 181 </body> | |
| 182 </html> |