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