Mercurial > repos > deepakjadmin > mayatool3_test2
comparison docs/scripts/html/InfoSequenceFiles.html @ 0:4816e4a8ae95 draft default tip
Uploaded
author | deepakjadmin |
---|---|
date | Wed, 20 Jan 2016 09:23:18 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:4816e4a8ae95 |
---|---|
1 <html> | |
2 <head> | |
3 <title>MayaChemTools:Documentation:InfoSequenceFiles.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="./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> | |
16 </table> | |
17 </div> | |
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 | "number, number, [number,...]"] | |
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 | "number,number,[number,...]"</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 "150,200,250,300,350" --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>, <a href="./ExtractFromSequenceFiles.html">ExtractFromSequenceFiles.pl</a>, <a href="./InfoAminoAcids.html">InfoAminoAcids.pl</a>, <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> </p><p> </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> <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> | |
157 </table> | |
158 </div> | |
159 <br /> | |
160 <center> | |
161 <img src="../../images/h2o2.png"> | |
162 </center> | |
163 </body> | |
164 </html> |