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3 <title>MayaChemTools:Documentation:SequenceFileUtil.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./SDFileUtil.html" title="SDFileUtil.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./StatisticsUtil.html" title="StatisticsUtil.html">Next</a></td><td width="34%" align="middle"><strong>SequenceFileUtil.pm</strong></td><td width="33%" align="right"><a href="././code/SequenceFileUtil.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/SequenceFileUtil.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/SequenceFileUtil.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/SequenceFileUtil.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/SequenceFileUtil.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>SequenceFileUtil</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use SequenceFileUtil ;</p>
26 <p>use SequenceFileUtil qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>SequenceFileUtil</strong> module provides the following functions:</p>
31 <p> <a href="#aresequencelengthsidentical">AreSequenceLengthsIdentical</a>, <a href="#calcuatepercentsequenceidentity">CalcuatePercentSequenceIdentity</a>
32 , <a href="#calculatepercentsequenceidentitymatrix">CalculatePercentSequenceIdentityMatrix</a>, <a href="#getlongestsequence">GetLongestSequence</a>, <a href="#getsequencelength">GetSequenceLength</a>
33 , <a href="#getshortestsequence">GetShortestSequence</a>, <a href="#isclustalwsequencefile">IsClustalWSequenceFile</a>, <a href="#isgapresidue">IsGapResidue</a>, <a href="#ismsfsequencefile">IsMSFSequenceFile</a>
34 , <a href="#ispirfastasequencefile">IsPIRFastaSequenceFile</a>, <a href="#ispearsonfastasequencefile">IsPearsonFastaSequenceFile</a>, <a href="#issupportedsequencefile">IsSupportedSequenceFile</a>
35 , <a href="#readclustalwsequencefile">ReadClustalWSequenceFile</a>, <a href="#readmsfsequencefile">ReadMSFSequenceFile</a>, <a href="#readpirfastasequencefile">ReadPIRFastaSequenceFile</a>
36 , <a href="#readpearsonfastasequencefile">ReadPearsonFastaSequenceFile</a>, <a href="#readsequencefile">ReadSequenceFile</a>, <a href="#removesequencealignmentgapcolumns">RemoveSequenceAlignmentGapColumns</a>
37 , <a href="#removesequencegaps">RemoveSequenceGaps</a>, <a href="#writepearsonfastasequencefile">WritePearsonFastaSequenceFile</a>
38 , <a href="#sequencefileutil module provides various methods to process sequence">SequenceFileUtil module provides various methods to process sequence</a>
39 , <a href="#files and retreive appropriate information.">files and retreive appropriate information.</a>
40 </p><p>
41 </p>
42 <h2>FUNCTIONS</h2>
43 <dl>
44 <dt><strong><a name="aresequencelengthsidentical" class="item"><strong>AreSequenceLengthsIdentical</strong></a></strong></dt>
45 <dd>
46 <div class="OptionsBox">
47 $Status = AreSequenceLengthsIdentical($SequencesDataRef);</div>
48 <p>Checks the lengths of all the sequences available in <em>SequencesDataRef</em> and returns 1
49 or 0 based whether lengths of all the sequence is same.</p>
50 </dd>
51 <dt><strong><a name="calcuatepercentsequenceidentity" class="item"><strong>CalcuatePercentSequenceIdentity</strong></a></strong></dt>
52 <dd>
53 <div class="OptionsBox">
54 $PercentIdentity =
55 AreSequenceLengthsIdenticalAreSequenceLengthsIdentical(
56 $Sequence1, $Sequence2, [$IgnoreGaps, $Precision]);</div>
57 <p>Returns percent identity between <em>Sequence1</em> and <em>Sequence2</em>. Optional arguments
58 <em>IgnoreGaps</em> and <em>Precision</em> control handling of gaps in sequences and precision of the
59 returned value. By default, gaps are ignored and precision is set up to 1 decimal.</p>
60 </dd>
61 <dt><strong><a name="calculatepercentsequenceidentitymatrix" class="item"><strong>CalculatePercentSequenceIdentityMatrix</strong></a></strong></dt>
62 <dd>
63 <div class="OptionsBox">
64 $IdentityMatrixDataRef = CalculatePercentSequenceIdentityMatrix(
65 $SequencesDataRef, [$IgnoreGaps,
66 $Precision]);</div>
67 <p>Calculate pairwise percent identity between all the sequences available in <em>SequencesDataRef</em>
68 and returns a reference to identity matrix hash. Optional arguments <em>IgnoreGaps</em> and
69 <em>Precision</em> control handling of gaps in sequences and precision of the returned value. By default, gaps
70 are ignored and precision is set up to 1 decimal.</p>
71 </dd>
72 <dt><strong><a name="getsequencelength" class="item"><strong>GetSequenceLength</strong></a></strong></dt>
73 <dd>
74 <div class="OptionsBox">
75 $SeqquenceLength = GetSequenceLength($Sequence, [$IgnoreGaps]);</div>
76 <p>Returns length of the specified sequence. Optional argument <em>IgnoreGaps</em> controls handling
77 of gaps. By default, gaps are ignored.</p>
78 </dd>
79 <dt><strong><a name="getshortestsequence" class="item"><strong>GetShortestSequence</strong></a></strong></dt>
80 <dd>
81 <div class="OptionsBox">
82 ($ID, $Sequence, $SeqLen, $Description) = GetShortestSequence(
83 &nbsp;&nbsp;&nbsp; $SequencesDataRef, [$IgnoreGaps]);</div>
84 <p>Checks the lengths of all the sequences available in $SequencesDataRef and returns $ID,
85 $Sequence, $SeqLen, and $Description values for the shortest sequence. Optional arguments $IgnoreGaps
86 controls handling of gaps in sequences. By default, gaps are ignored.</p>
87 </dd>
88 <dt><strong><a name="getlongestsequence" class="item"><strong>GetLongestSequence</strong></a></strong></dt>
89 <dd>
90 <div class="OptionsBox">
91 ($ID, $Sequence, $SeqLen, $Description) = GetLongestSequence(
92 &nbsp;&nbsp;&nbsp; $SequencesDataRef, [$IgnoreGaps]);</div>
93 <p>Checks the lengths of all the sequences available in <em>SequencesDataRef</em> and returns <strong>ID</strong>,
94 <strong>Sequence</strong>, <strong>SeqLen</strong>, and <strong>Description</strong> values for the longest sequence. Optional argument
95 $<em>IgnoreGaps</em> controls handling of gaps in sequences. By default, gaps are ignored.</p>
96 </dd>
97 <dt><strong><a name="isgapresidue" class="item"><strong>IsGapResidue</strong></a></strong></dt>
98 <dd>
99 <div class="OptionsBox">
100 $Status = AreSequenceLengthsIdentical($Residue);</div>
101 <p>Returns 1 or 0 based on whether <em>Residue</em> corresponds to a gap. Any character other than A to Z is
102 considered a gap residue.</p>
103 </dd>
104 <dt><strong><a name="issupportedsequencefile" class="item"><strong>IsSupportedSequenceFile</strong></a></strong></dt>
105 <dd>
106 <div class="OptionsBox">
107 $Status = IsSupportedSequenceFile($SequenceFile);</div>
108 <p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to a supported sequence
109 format.</p>
110 </dd>
111 <dt><strong><a name="isclustalwsequencefile" class="item"><strong>IsClustalWSequenceFile</strong></a></strong></dt>
112 <dd>
113 <div class="OptionsBox">
114 $Status = IsClustalWSequenceFile($SequenceFile);</div>
115 <p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to Clustal sequence alignment
116 format.</p>
117 </dd>
118 <dt><strong><a name="ispearsonfastasequencefile" class="item"><strong>IsPearsonFastaSequenceFile</strong></a></strong></dt>
119 <dd>
120 <div class="OptionsBox">
121 $Status = IsPearsonFastaSequenceFile($SequenceFile);</div>
122 <p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to Pearson FASTA sequence
123 format.</p>
124 </dd>
125 <dt><strong><a name="ispirfastasequencefile" class="item"><strong>IsPIRFastaSequenceFile</strong></a></strong></dt>
126 <dd>
127 <div class="OptionsBox">
128 $Status = IsPIRFastaSequenceFile($SequenceFile);</div>
129 <p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to PIR FASTA sequence
130 format.</p>
131 </dd>
132 <dt><strong><a name="ismsfsequencefile" class="item"><strong>IsMSFSequenceFile</strong></a></strong></dt>
133 <dd>
134 <div class="OptionsBox">
135 $Status = IsClustalWSequenceFile($SequenceFile);</div>
136 <p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to MSF sequence alignment
137 format.</p>
138 </dd>
139 <dt><strong><a name="readsequencefile" class="item"><strong>ReadSequenceFile</strong></a></strong></dt>
140 <dd>
141 <div class="OptionsBox">
142 $SequenceDataMapRef = ReadSequenceFile($SequenceFile);</div>
143 <p>Reads <em>SequenceFile</em> and returns reference to a hash containing following key/value
144 pairs:</p>
145 <div class="OptionsBox">
146 $SequenceDataMapRef-&gt;{IDs} - Array of sequence IDs
147 <br/> $SequenceDataMapRef-&gt;{Count} - Number of sequences
148 <br/> $SequenceDataMapRef-&gt;{Description}{$ID} - Sequence description
149 <br/> $SequenceDataMapRef-&gt;{Sequence}{$ID} - Sequence for a specific ID
150 <br/> $SequenceDataMapRef-&gt;{Sequence}{InputFileType} - File format</div>
151 </dd>
152 <dt><strong><a name="readclustalwsequencefile" class="item"><strong>ReadClustalWSequenceFile</strong></a></strong></dt>
153 <dd>
154 <div class="OptionsBox">
155 $SequenceDataMapRef = ReadClustalWSequenceFile($SequenceFile);</div>
156 <p>Reads ClustalW <em>SequenceFile</em> and returns reference to a hash containing following key/value
157 pairs as describes in <strong>ReadSequenceFile</strong> method.</p>
158 </dd>
159 <dt><strong><a name="readmsfsequencefile" class="item"><strong>ReadMSFSequenceFile</strong></a></strong></dt>
160 <dd>
161 <div class="OptionsBox">
162 $SequenceDataMapRef = ReadMSFSequenceFile($SequenceFile);</div>
163 <p>Reads MSF <em>SequenceFile</em> and returns reference to a hash containing following key/value
164 pairs as describes in <strong>ReadSequenceFile</strong> method.</p>
165 </dd>
166 <dt><strong><a name="readpirfastasequencefile" class="item"><strong>ReadPIRFastaSequenceFile</strong></a></strong></dt>
167 <dd>
168 <div class="OptionsBox">
169 $SequenceDataMapRef = ReadPIRFastaSequenceFile($SequenceFile);</div>
170 <p>Reads PIR FASTA <em>SequenceFile</em> and returns reference to a hash containing following key/value
171 pairs as describes in <strong>ReadSequenceFile</strong> method.</p>
172 </dd>
173 <dt><strong><a name="readpearsonfastasequencefile" class="item"><strong>ReadPearsonFastaSequenceFile</strong></a></strong></dt>
174 <dd>
175 <div class="OptionsBox">
176 $SequenceDataMapRef = ReadPearsonFastaSequenceFile($SequenceFile);</div>
177 <p>Reads Pearson FASTA <em>SequenceFile</em> and returns reference to a hash containing following key/value
178 pairs as describes in <strong>ReadSequenceFile</strong> method.</p>
179 </dd>
180 <dt><strong><a name="removesequencegaps" class="item"><strong>RemoveSequenceGaps</strong></a></strong></dt>
181 <dd>
182 <div class="OptionsBox">
183 $SeqWithoutGaps = RemoveSequenceGaps($Sequence);</div>
184 <p>Removes gaps from <em>Sequence</em> and return a sequence without any gaps.</p>
185 </dd>
186 <dt><strong><a name="removesequencealignmentgapcolumns" class="item"><strong>RemoveSequenceAlignmentGapColumns</strong></a></strong></dt>
187 <dd>
188 <div class="OptionsBox">
189 $NewAlignmentDataMapRef = RemoveSequenceAlignmentGapColumns(
190 $AlignmentDataMapRef);</div>
191 <p>Using input alignment data map ref containing following keys, generate a new hash with
192 same set of keys after residue columns containg only gaps have been removed:</p>
193 <div class="OptionsBox">
194 {IDs} : Array of IDs in order as they appear in file
195 <br/> {Count}: ID count
196 <br/> {Description}{$ID} : Description data
197 <br/> {Sequence}{$ID} : Sequence data</div>
198 </dd>
199 <dt><strong><a name="writepearsonfastasequencefile" class="item"><strong>WritePearsonFastaSequenceFile</strong></a></strong></dt>
200 <dd>
201 <div class="OptionsBox">
202 WritePearsonFastaSequenceFile($SequenceFileName, $SequenceDataRef,
203 [$MaxLength]);</div>
204 <p>Using sequence data specified via <em>SequenceDataRef</em>, write out a Pearson FASTA sequence
205 file. Optional argument <em>MaxLength</em> controls maximum length sequence in each line; default is
206 80.</p>
207 </dd>
208 </dl>
209 <p>
210 </p>
211 <h2>AUTHOR</h2>
212 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
213 <p>
214 </p>
215 <h2>SEE ALSO</h2>
216 <p><a href="./PDBFileUtil.html">PDBFileUtil.pm</a>
217 </p>
218 <p>
219 </p>
220 <h2>COPYRIGHT</h2>
221 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
222 <p>This file is part of MayaChemTools.</p>
223 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
224 the terms of the GNU Lesser General Public License as published by the Free
225 Software Foundation; either version 3 of the License, or (at your option)
226 any later version.</p>
227 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
228 <table width="100%" border=0 cellpadding=0 cellspacing=2>
229 <tr align="left" valign="top"><td width="33%" align="left"><a href="./SDFileUtil.html" title="SDFileUtil.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./StatisticsUtil.html" title="StatisticsUtil.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>SequenceFileUtil.pm</strong></td></tr>
230 </table>
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