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3 <title>MayaChemTools:Documentation:InfoSequenceFiles.pl</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./InfoSDFiles.html" title="InfoSDFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>&nbsp;|&nbsp;<a href="./../pdf/InfoSequenceFiles.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/InfoSequenceFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/InfoSequenceFiles.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/InfoSequenceFiles.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>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 | &quot;number, number, [number,...]&quot;]
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 | &quot;number,number,[number,...]&quot;</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 &quot;150,200,250,300,350&quot; --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>,&nbsp<a href="./ExtractFromSequenceFiles.html">ExtractFromSequenceFiles.pl</a>,&nbsp<a href="./InfoAminoAcids.html">InfoAminoAcids.pl</a>,&nbsp<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>&nbsp</p><p>&nbsp</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>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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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