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<h2>NAME</h2>
<p>SequenceFileUtil</p>
<p>
</p>
<h2>SYNOPSIS</h2>
<p>use SequenceFileUtil ;</p>
<p>use SequenceFileUtil qw(:all);</p>
<p>
</p>
<h2>DESCRIPTION</h2>
<p><strong>SequenceFileUtil</strong> module provides the following functions:</p>
<p> <a href="#aresequencelengthsidentical">AreSequenceLengthsIdentical</a>, <a href="#calcuatepercentsequenceidentity">CalcuatePercentSequenceIdentity</a>
, <a href="#calculatepercentsequenceidentitymatrix">CalculatePercentSequenceIdentityMatrix</a>, <a href="#getlongestsequence">GetLongestSequence</a>, <a href="#getsequencelength">GetSequenceLength</a>
, <a href="#getshortestsequence">GetShortestSequence</a>, <a href="#isclustalwsequencefile">IsClustalWSequenceFile</a>, <a href="#isgapresidue">IsGapResidue</a>, <a href="#ismsfsequencefile">IsMSFSequenceFile</a>
, <a href="#ispirfastasequencefile">IsPIRFastaSequenceFile</a>, <a href="#ispearsonfastasequencefile">IsPearsonFastaSequenceFile</a>, <a href="#issupportedsequencefile">IsSupportedSequenceFile</a>
, <a href="#readclustalwsequencefile">ReadClustalWSequenceFile</a>, <a href="#readmsfsequencefile">ReadMSFSequenceFile</a>, <a href="#readpirfastasequencefile">ReadPIRFastaSequenceFile</a>
, <a href="#readpearsonfastasequencefile">ReadPearsonFastaSequenceFile</a>, <a href="#readsequencefile">ReadSequenceFile</a>, <a href="#removesequencealignmentgapcolumns">RemoveSequenceAlignmentGapColumns</a>
, <a href="#removesequencegaps">RemoveSequenceGaps</a>, <a href="#writepearsonfastasequencefile">WritePearsonFastaSequenceFile</a>
, <a href="#sequencefileutil module provides various methods to process sequence">SequenceFileUtil module provides various methods to process sequence</a>
, <a href="#files and retreive appropriate information.">files and retreive appropriate information.</a>
</p><p>
</p>
<h2>FUNCTIONS</h2>
<dl>
<dt><strong><a name="aresequencelengthsidentical" class="item"><strong>AreSequenceLengthsIdentical</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $Status = AreSequenceLengthsIdentical($SequencesDataRef);</div>
<p>Checks the lengths of all the sequences available in <em>SequencesDataRef</em> and returns 1
or 0 based whether lengths of all the sequence is same.</p>
</dd>
<dt><strong><a name="calcuatepercentsequenceidentity" class="item"><strong>CalcuatePercentSequenceIdentity</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $PercentIdentity =
       AreSequenceLengthsIdenticalAreSequenceLengthsIdentical(
          $Sequence1, $Sequence2, [$IgnoreGaps, $Precision]);</div>
<p>Returns percent identity between <em>Sequence1</em> and <em>Sequence2</em>. Optional arguments
<em>IgnoreGaps</em> and <em>Precision</em> control handling of gaps in sequences and precision of the
returned value. By default, gaps are ignored and precision is set up to 1 decimal.</p>
</dd>
<dt><strong><a name="calculatepercentsequenceidentitymatrix" class="item"><strong>CalculatePercentSequenceIdentityMatrix</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $IdentityMatrixDataRef = CalculatePercentSequenceIdentityMatrix(
                             $SequencesDataRef, [$IgnoreGaps,
                             $Precision]);</div>
<p>Calculate pairwise percent identity between all the sequences available in <em>SequencesDataRef</em>
and returns a reference to identity matrix hash. Optional arguments <em>IgnoreGaps</em> and
<em>Precision</em> control handling of gaps in sequences and precision of the returned value. By default, gaps
are ignored and precision is set up to 1 decimal.</p>
</dd>
<dt><strong><a name="getsequencelength" class="item"><strong>GetSequenceLength</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $SeqquenceLength = GetSequenceLength($Sequence, [$IgnoreGaps]);</div>
<p>Returns length of the specified sequence. Optional argument <em>IgnoreGaps</em> controls handling
of gaps. By default, gaps are ignored.</p>
</dd>
<dt><strong><a name="getshortestsequence" class="item"><strong>GetShortestSequence</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
   ($ID, $Sequence, $SeqLen, $Description) = GetShortestSequence(
&nbsp;&nbsp;&nbsp;       $SequencesDataRef, [$IgnoreGaps]);</div>
<p>Checks the lengths of all the sequences available in $SequencesDataRef and returns $ID,
$Sequence, $SeqLen, and $Description values for the shortest sequence. Optional arguments $IgnoreGaps
controls handling of gaps in sequences. By default, gaps are ignored.</p>
</dd>
<dt><strong><a name="getlongestsequence" class="item"><strong>GetLongestSequence</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
   ($ID, $Sequence, $SeqLen, $Description) = GetLongestSequence(
&nbsp;&nbsp;&nbsp;       $SequencesDataRef, [$IgnoreGaps]);</div>
<p>Checks the lengths of all the sequences available in <em>SequencesDataRef</em> and returns <strong>ID</strong>,
<strong>Sequence</strong>, <strong>SeqLen</strong>, and <strong>Description</strong> values for the longest sequence. Optional argument
$<em>IgnoreGaps</em> controls handling of gaps in sequences. By default, gaps are ignored.</p>
</dd>
<dt><strong><a name="isgapresidue" class="item"><strong>IsGapResidue</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $Status = AreSequenceLengthsIdentical($Residue);</div>
<p>Returns 1 or 0 based on whether <em>Residue</em> corresponds to a gap. Any character other than A to Z is
considered a gap residue.</p>
</dd>
<dt><strong><a name="issupportedsequencefile" class="item"><strong>IsSupportedSequenceFile</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $Status = IsSupportedSequenceFile($SequenceFile);</div>
<p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to a supported sequence
format.</p>
</dd>
<dt><strong><a name="isclustalwsequencefile" class="item"><strong>IsClustalWSequenceFile</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $Status = IsClustalWSequenceFile($SequenceFile);</div>
<p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to Clustal sequence alignment
format.</p>
</dd>
<dt><strong><a name="ispearsonfastasequencefile" class="item"><strong>IsPearsonFastaSequenceFile</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $Status = IsPearsonFastaSequenceFile($SequenceFile);</div>
<p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to Pearson FASTA sequence
format.</p>
</dd>
<dt><strong><a name="ispirfastasequencefile" class="item"><strong>IsPIRFastaSequenceFile</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $Status = IsPIRFastaSequenceFile($SequenceFile);</div>
<p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to PIR FASTA sequence
format.</p>
</dd>
<dt><strong><a name="ismsfsequencefile" class="item"><strong>IsMSFSequenceFile</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $Status = IsClustalWSequenceFile($SequenceFile);</div>
<p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to MSF sequence alignment
format.</p>
</dd>
<dt><strong><a name="readsequencefile" class="item"><strong>ReadSequenceFile</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $SequenceDataMapRef = ReadSequenceFile($SequenceFile);</div>
<p>Reads <em>SequenceFile</em> and returns reference to a hash containing following key/value
pairs:</p>
<div class="OptionsBox">
    $SequenceDataMapRef-&gt;{IDs} - Array of sequence IDs
<br/>    $SequenceDataMapRef-&gt;{Count} - Number of sequences
<br/>    $SequenceDataMapRef-&gt;{Description}{$ID} - Sequence description
<br/>    $SequenceDataMapRef-&gt;{Sequence}{$ID} - Sequence for a specific ID
<br/>    $SequenceDataMapRef-&gt;{Sequence}{InputFileType} - File format</div>
</dd>
<dt><strong><a name="readclustalwsequencefile" class="item"><strong>ReadClustalWSequenceFile</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $SequenceDataMapRef = ReadClustalWSequenceFile($SequenceFile);</div>
<p>Reads ClustalW <em>SequenceFile</em> and returns reference to a hash containing following key/value
pairs as describes in <strong>ReadSequenceFile</strong> method.</p>
</dd>
<dt><strong><a name="readmsfsequencefile" class="item"><strong>ReadMSFSequenceFile</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $SequenceDataMapRef = ReadMSFSequenceFile($SequenceFile);</div>
<p>Reads MSF <em>SequenceFile</em> and returns reference to a hash containing following key/value
pairs as describes in <strong>ReadSequenceFile</strong> method.</p>
</dd>
<dt><strong><a name="readpirfastasequencefile" class="item"><strong>ReadPIRFastaSequenceFile</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $SequenceDataMapRef = ReadPIRFastaSequenceFile($SequenceFile);</div>
<p>Reads PIR FASTA <em>SequenceFile</em> and returns reference to a hash containing following key/value
pairs as describes in <strong>ReadSequenceFile</strong> method.</p>
</dd>
<dt><strong><a name="readpearsonfastasequencefile" class="item"><strong>ReadPearsonFastaSequenceFile</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $SequenceDataMapRef = ReadPearsonFastaSequenceFile($SequenceFile);</div>
<p>Reads Pearson FASTA <em>SequenceFile</em> and returns reference to a hash containing following key/value
pairs as describes in <strong>ReadSequenceFile</strong> method.</p>
</dd>
<dt><strong><a name="removesequencegaps" class="item"><strong>RemoveSequenceGaps</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $SeqWithoutGaps = RemoveSequenceGaps($Sequence);</div>
<p>Removes gaps from <em>Sequence</em> and return a sequence without any gaps.</p>
</dd>
<dt><strong><a name="removesequencealignmentgapcolumns" class="item"><strong>RemoveSequenceAlignmentGapColumns</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $NewAlignmentDataMapRef = RemoveSequenceAlignmentGapColumns(
                              $AlignmentDataMapRef);</div>
<p>Using input alignment data map ref containing following keys, generate a new hash with
same set of keys after residue columns containg only gaps have been removed:</p>
<div class="OptionsBox">
    {IDs} : Array of IDs in order as they appear in file
<br/>    {Count}: ID count
<br/>    {Description}{$ID} : Description data
<br/>    {Sequence}{$ID} : Sequence data</div>
</dd>
<dt><strong><a name="writepearsonfastasequencefile" class="item"><strong>WritePearsonFastaSequenceFile</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    WritePearsonFastaSequenceFile($SequenceFileName, $SequenceDataRef,
                                  [$MaxLength]);</div>
<p>Using sequence data specified via <em>SequenceDataRef</em>, write out a Pearson FASTA sequence
file. Optional argument <em>MaxLength</em> controls maximum length sequence in each line; default is
80.</p>
</dd>
</dl>
<p>
</p>
<h2>AUTHOR</h2>
<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
<p>
</p>
<h2>SEE ALSO</h2>
<p><a href="./PDBFileUtil.html">PDBFileUtil.pm</a>
</p>
<p>
</p>
<h2>COPYRIGHT</h2>
<p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
<p>This file is part of MayaChemTools.</p>
<p>MayaChemTools is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option)
any later version.</p>
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