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3 <title>MayaChemTools:Documentation:ExtractFromSequenceFiles.pl</title>
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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="./ExtractFromSDFiles.html" title="ExtractFromSDFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtractFromTextFiles.html" title="ExtractFromTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>ExtractFromSequenceFiles.pl</strong></td><td width="33%" align="right"><a href="././code/ExtractFromSequenceFiles.html" title="View source code">Code</a> | <a href="./../pdf/ExtractFromSequenceFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ExtractFromSequenceFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ExtractFromSequenceFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ExtractFromSequenceFiles.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>ExtractFromSequenceFiles.pl - Extract data from 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>ExtractFromSequenceFiles.pl SequenceFile(s) AlignmentFile(s)...</p>
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26 <p>ExtractFromSequenceFiles.pl [<strong>-h, --help</strong>] [<strong>-i, --IgnoreGaps</strong> yes | no]
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27 [<strong>-m, --mode</strong> SequenceID | SequenceNum | SequenceNumRange] [<strong>-o, --overwrite</strong>]
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28 [<strong>-r, --root</strong> rootname] [<strong>-s, --Sequences</strong> "SequenceID, [SequenceID,...]" | "SequenceNum, [SequenceNum,...]" |
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29 "StartingSeqNum, EndingSeqNum"] [<strong>--SequenceIDMatch</strong> Exact | Relaxed]
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30 [<strong>-w, --WorkingDir</strong> dirname] SequenceFile(s) AlignmentFile(s)...</p>
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31 <p>
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32 </p>
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33 <h2>DESCRIPTION</h2>
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34 <p>Extract specific data from <em>SequenceFile(s) and AlignmentFile(s)</em> and generate
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35 FASTA files. You can extract sequences using sequence IDs or sequence numbers.</p>
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36 <p>The file names are separated by spaces. All the sequence files in a current directory can
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37 be specified by <em>*.aln</em>, <em>*.msf</em>, <em>*.fasta</em>, <em>*.fta</em>, <em>*.pir</em> or any other supported
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38 formats; additionally, <em>DirName</em> corresponds to all the sequence files in the current directory
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39 with any of the supported file extension: <em>.aln, .msf, .fasta, .fta, and .pir</em>.</p>
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40 <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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41 and <em>NBRF/PIR</em>. Instead of using file extensions, file formats are detected by parsing the contents
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42 of <em>SequenceFile(s) and AlignmentFile(s)</em>.</p>
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43 <p>
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44 </p>
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45 <h2>OPTIONS</h2>
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46 <dl>
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47 <dt><strong><strong>-h, --help</strong></strong></dt>
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48 <dd>
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49 <p>Print this help message.</p>
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50 </dd>
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51 <dt><strong><strong>-i, --IgnoreGaps</strong> <em>yes | no</em></strong></dt>
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52 <dd>
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53 <p>Ignore gaps or gap columns during during generation of new sequence or alignment file(s).
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54 Possible values: <em>yes or no</em>. Default value: <em>yes</em>.</p>
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55 <p>In order to remove gap columns, length of all the sequence must be same; otherwise,
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56 this option is ignored.</p>
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57 </dd>
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58 <dt><strong><strong>-m, --mode</strong> <em>SequenceID | SequenceNum | SequenceNumRange</em></strong></dt>
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59 <dd>
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60 <p>Specify how to extract data from sequence files: extract sequences using sequence
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61 IDs or sequence numbers. Possible values: <em>SequenceID | SequenceNum
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62 | SequenceNumRange</em>. Default: <em>SequenceNum</em> with value of 1.</p>
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63 <p>The sequence numbers correspond to position of sequences starting from 1 for first sequence
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64 in <em>SequenceFile(s) and AlignmentFile(s)</em>.</p>
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65 </dd>
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66 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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67 <dd>
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68 <p>Overwrite existing files.</p>
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69 </dd>
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70 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
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71 <dd>
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72 <p>New sequence file name is generated using the root: <Root><Mode>.<Ext>. Default new file:
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73 <SequenceFileName><Mode>.<Ext>. This option is ignored for multiple input files.</p>
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74 </dd>
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75 <dt><strong><strong>-s, --Sequences</strong> <em>"SequenceID,[SequenceID,...]" | "SequenceNum,[SequenceNum,...]" | "StartingSeqNum,EndingSeqNum"</em></strong></dt>
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76 <dd>
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77 <p>This value is <strong>-m, --mode</strong> specific. In general, it's a comma delimites list of sequence IDs or sequence
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78 numbers.</p>
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79 <p>For <em>SequenceID</em> value of <strong>-m, --mode</strong> option, input value format is: <em>SequenceID,...</em>. Examples:</p>
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80 <div class="OptionsBox">
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81 ACHE_BOVIN
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82 <br/> ACHE_BOVIN,ACHE_HUMAN</div>
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83 <p>For <em>SequenceNum</em> value of <strong>-m, --mode</strong> option, input value format is: <em>SequenceNum,...</em>. Examples:</p>
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84 <div class="OptionsBox">
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85 2
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86 <br/> 1,5</div>
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87 <p>For <em>SequenceNum</em> value of <strong>-m, --mode</strong> option, input value format is: <em>StaringSeqNum,EndingSeqNum</em>. Examples:</p>
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88 <div class="OptionsBox">
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89 2,4</div>
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90 </dd>
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91 <dt><strong><strong>--SequenceIDMatch</strong> <em>Exact | Relaxed</em></strong></dt>
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92 <dd>
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93 <p>Sequence IDs matching criterion during <em>SequenceID</em> value of <strong>-m, --mode</strong> option: match
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94 specified sequence ID exactly or as sub string against sequence IDs in the files. Possible
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95 values: <em>Exact | Relaxed</em>. Default: <em>Relaxed</em>. Sequence ID match is case insenstitive
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96 during both options.</p>
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97 </dd>
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98 <dt><strong><strong>--SequenceLength</strong> <em>number</em></strong></dt>
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99 <dd>
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100 <p>Maximum sequence length per line in sequence file(s). Default: <em>80</em>.</p>
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101 </dd>
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102 <dt><strong><strong>-w --WorkingDir</strong> <em>text</em></strong></dt>
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103 <dd>
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104 <p>Location of working directory. Default: current directory.</p>
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105 </dd>
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106 </dl>
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107 <p>
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108 </p>
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109 <h2>EXAMPLES</h2>
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110 <p>To extract first sequence from Sample1.fasta sequence file and generate Sample1SequenceNum.fasta
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111 sequence file, type:</p>
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112 <div class="ExampleBox">
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113 % ExtractFromSequenceFiles.pl -o Sample1.fasta</div>
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114 <p>To extract first sequence from Sample1.aln alignment file and generate Sample1SequenceNum.fasta
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115 sequence file without any column gaps, type:</p>
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116 <div class="ExampleBox">
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117 % ExtractFromSequenceFiles.pl -o Sample1.aln</div>
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118 <p>To extract first sequence from Sample1.aln alignment file and generate Sample1SequenceNum.fasta
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119 sequence file with column gaps, type:</p>
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120 <div class="ExampleBox">
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121 % ExtractFromSequenceFiles.pl --IgnroreGaps No -o Sample1.aln</div>
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122 <p>To extract sequence number 1 and 4 from Sample1.fasta sequence file and generate
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123 Sample1SequenceNum.fasta sequence file, type:</p>
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124 <div class="ExampleBox">
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125 % ExtractFromSequenceFiles.pl -o -m SequenceNum --Sequences 1,4
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126 -o Sample1.fasta</div>
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127 <p>To extract sequences from sequence number 1 to 4 from Sample1.fasta sequence file and generate
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128 Sample1SequenceNumRange.fasta sequence file, type:</p>
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129 <div class="ExampleBox">
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130 % ExtractFromSequenceFiles.pl -o -m SequenceNumRange --Sequences
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131 1,4 -o Sample1.fasta</div>
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132 <p>To extract sequence ID "Q9P993/104-387" from sequence from Sample1.fasta sequence file and generate
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133 Sample1SequenceID.fasta sequence file, type:</p>
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134 <div class="ExampleBox">
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135 % ExtractFromSequenceFiles.pl -o -m SequenceID --Sequences
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136 "Q9P993/104-387" --SequenceIDMatch Exact -o Sample1.fasta</div>
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137 <p>
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138 </p>
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139 <h2>AUTHOR</h2>
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140 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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141 <p>
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142 </p>
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143 <h2>SEE ALSO</h2>
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144 <p><a href="./AnalyzeSequenceFilesData.html">AnalyzeSequenceFilesData.pl</a>, <a href="./InfoSequenceFiles.html">InfoSequenceFiles.pl</a>
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145 </p>
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146 <p>
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147 </p>
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148 <h2>COPYRIGHT</h2>
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149 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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150 <p>This file is part of MayaChemTools.</p>
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151 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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152 the terms of the GNU Lesser General Public License as published by the Free
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153 Software Foundation; either version 3 of the License, or (at your option)
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154 any later version.</p>
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155 <p> </p><p> </p><div class="DocNav">
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156 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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157 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtractFromSDFiles.html" title="ExtractFromSDFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtractFromTextFiles.html" title="ExtractFromTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ExtractFromSequenceFiles.pl</strong></td></tr>
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158 </table>
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159 </div>
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160 <br />
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161 <center>
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162 <img src="../../images/h2o2.png">
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