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3 <title>MayaChemTools:Documentation:ExtractFromSequenceFiles.pl</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtractFromSDFiles.html" title="ExtractFromSDFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>&nbsp;|&nbsp;<a href="./../pdf/ExtractFromSequenceFiles.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/ExtractFromSequenceFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/ExtractFromSequenceFiles.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/ExtractFromSequenceFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>ExtractFromSequenceFiles.pl - Extract data from sequence and alignment files</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>ExtractFromSequenceFiles.pl SequenceFile(s) AlignmentFile(s)...</p>
26 <p>ExtractFromSequenceFiles.pl [<strong>-h, --help</strong>] [<strong>-i, --IgnoreGaps</strong> yes | no]
27 [<strong>-m, --mode</strong> SequenceID | SequenceNum | SequenceNumRange] [<strong>-o, --overwrite</strong>]
28 [<strong>-r, --root</strong> rootname] [<strong>-s, --Sequences</strong> &quot;SequenceID, [SequenceID,...]&quot; | &quot;SequenceNum, [SequenceNum,...]&quot; |
29 &quot;StartingSeqNum, EndingSeqNum&quot;] [<strong>--SequenceIDMatch</strong> Exact | Relaxed]
30 [<strong>-w, --WorkingDir</strong> dirname] SequenceFile(s) AlignmentFile(s)...</p>
31 <p>
32 </p>
33 <h2>DESCRIPTION</h2>
34 <p>Extract specific data from <em>SequenceFile(s) and AlignmentFile(s)</em> and generate
35 FASTA files. You can extract sequences using sequence IDs or sequence numbers.</p>
36 <p>The file names are separated by spaces. All the sequence files in a current directory can
37 be specified by <em>*.aln</em>, <em>*.msf</em>, <em>*.fasta</em>, <em>*.fta</em>, <em>*.pir</em> or any other supported
38 formats; additionally, <em>DirName</em> corresponds to all the sequence files in the current directory
39 with any of the supported file extension: <em>.aln, .msf, .fasta, .fta, and .pir</em>.</p>
40 <p>Supported sequence formats are: <em>ALN/CLustalW</em>, <em>GCG/MSF</em>, <em>PILEUP/MSF</em>, <em>Pearson/FASTA</em>,
41 and <em>NBRF/PIR</em>. Instead of using file extensions, file formats are detected by parsing the contents
42 of <em>SequenceFile(s) and AlignmentFile(s)</em>.</p>
43 <p>
44 </p>
45 <h2>OPTIONS</h2>
46 <dl>
47 <dt><strong><strong>-h, --help</strong></strong></dt>
48 <dd>
49 <p>Print this help message.</p>
50 </dd>
51 <dt><strong><strong>-i, --IgnoreGaps</strong> <em>yes | no</em></strong></dt>
52 <dd>
53 <p>Ignore gaps or gap columns during during generation of new sequence or alignment file(s).
54 Possible values: <em>yes or no</em>. Default value: <em>yes</em>.</p>
55 <p>In order to remove gap columns, length of all the sequence must be same; otherwise,
56 this option is ignored.</p>
57 </dd>
58 <dt><strong><strong>-m, --mode</strong> <em>SequenceID | SequenceNum | SequenceNumRange</em></strong></dt>
59 <dd>
60 <p>Specify how to extract data from sequence files: extract sequences using sequence
61 IDs or sequence numbers. Possible values: <em>SequenceID | SequenceNum
62 | SequenceNumRange</em>. Default: <em>SequenceNum</em> with value of 1.</p>
63 <p>The sequence numbers correspond to position of sequences starting from 1 for first sequence
64 in <em>SequenceFile(s) and AlignmentFile(s)</em>.</p>
65 </dd>
66 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
67 <dd>
68 <p>Overwrite existing files.</p>
69 </dd>
70 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
71 <dd>
72 <p>New sequence file name is generated using the root: &lt;Root&gt;&lt;Mode&gt;.&lt;Ext&gt;. Default new file:
73 &lt;SequenceFileName&gt;&lt;Mode&gt;.&lt;Ext&gt;. This option is ignored for multiple input files.</p>
74 </dd>
75 <dt><strong><strong>-s, --Sequences</strong> <em>&quot;SequenceID,[SequenceID,...]&quot; | &quot;SequenceNum,[SequenceNum,...]&quot; | &quot;StartingSeqNum,EndingSeqNum&quot;</em></strong></dt>
76 <dd>
77 <p>This value is <strong>-m, --mode</strong> specific. In general, it's a comma delimites list of sequence IDs or sequence
78 numbers.</p>
79 <p>For <em>SequenceID</em> value of <strong>-m, --mode</strong> option, input value format is: <em>SequenceID,...</em>. Examples:</p>
80 <div class="OptionsBox">
81 ACHE_BOVIN
82 <br/> ACHE_BOVIN,ACHE_HUMAN</div>
83 <p>For <em>SequenceNum</em> value of <strong>-m, --mode</strong> option, input value format is: <em>SequenceNum,...</em>. Examples:</p>
84 <div class="OptionsBox">
85 2
86 <br/> 1,5</div>
87 <p>For <em>SequenceNum</em> value of <strong>-m, --mode</strong> option, input value format is: <em>StaringSeqNum,EndingSeqNum</em>. Examples:</p>
88 <div class="OptionsBox">
89 2,4</div>
90 </dd>
91 <dt><strong><strong>--SequenceIDMatch</strong> <em>Exact | Relaxed</em></strong></dt>
92 <dd>
93 <p>Sequence IDs matching criterion during <em>SequenceID</em> value of <strong>-m, --mode</strong> option: match
94 specified sequence ID exactly or as sub string against sequence IDs in the files. Possible
95 values: <em>Exact | Relaxed</em>. Default: <em>Relaxed</em>. Sequence ID match is case insenstitive
96 during both options.</p>
97 </dd>
98 <dt><strong><strong>--SequenceLength</strong> <em>number</em></strong></dt>
99 <dd>
100 <p>Maximum sequence length per line in sequence file(s). Default: <em>80</em>.</p>
101 </dd>
102 <dt><strong><strong>-w --WorkingDir</strong> <em>text</em></strong></dt>
103 <dd>
104 <p>Location of working directory. Default: current directory.</p>
105 </dd>
106 </dl>
107 <p>
108 </p>
109 <h2>EXAMPLES</h2>
110 <p>To extract first sequence from Sample1.fasta sequence file and generate Sample1SequenceNum.fasta
111 sequence file, type:</p>
112 <div class="ExampleBox">
113 % ExtractFromSequenceFiles.pl -o Sample1.fasta</div>
114 <p>To extract first sequence from Sample1.aln alignment file and generate Sample1SequenceNum.fasta
115 sequence file without any column gaps, type:</p>
116 <div class="ExampleBox">
117 % ExtractFromSequenceFiles.pl -o Sample1.aln</div>
118 <p>To extract first sequence from Sample1.aln alignment file and generate Sample1SequenceNum.fasta
119 sequence file with column gaps, type:</p>
120 <div class="ExampleBox">
121 % ExtractFromSequenceFiles.pl --IgnroreGaps No -o Sample1.aln</div>
122 <p>To extract sequence number 1 and 4 from Sample1.fasta sequence file and generate
123 Sample1SequenceNum.fasta sequence file, type:</p>
124 <div class="ExampleBox">
125 % ExtractFromSequenceFiles.pl -o -m SequenceNum --Sequences 1,4
126 -o Sample1.fasta</div>
127 <p>To extract sequences from sequence number 1 to 4 from Sample1.fasta sequence file and generate
128 Sample1SequenceNumRange.fasta sequence file, type:</p>
129 <div class="ExampleBox">
130 % ExtractFromSequenceFiles.pl -o -m SequenceNumRange --Sequences
131 1,4 -o Sample1.fasta</div>
132 <p>To extract sequence ID &quot;Q9P993/104-387&quot; from sequence from Sample1.fasta sequence file and generate
133 Sample1SequenceID.fasta sequence file, type:</p>
134 <div class="ExampleBox">
135 % ExtractFromSequenceFiles.pl -o -m SequenceID --Sequences
136 &quot;Q9P993/104-387&quot; --SequenceIDMatch Exact -o Sample1.fasta</div>
137 <p>
138 </p>
139 <h2>AUTHOR</h2>
140 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
141 <p>
142 </p>
143 <h2>SEE ALSO</h2>
144 <p><a href="./AnalyzeSequenceFilesData.html">AnalyzeSequenceFilesData.pl</a>,&nbsp<a href="./InfoSequenceFiles.html">InfoSequenceFiles.pl</a>
145 </p>
146 <p>
147 </p>
148 <h2>COPYRIGHT</h2>
149 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
150 <p>This file is part of MayaChemTools.</p>
151 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
152 the terms of the GNU Lesser General Public License as published by the Free
153 Software Foundation; either version 3 of the License, or (at your option)
154 any later version.</p>
155 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
156 <table width="100%" border=0 cellpadding=0 cellspacing=2>
157 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtractFromSDFiles.html" title="ExtractFromSDFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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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