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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/SequenceFileUtil.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,237 @@ +<html> +<head> +<title>MayaChemTools:Documentation:SequenceFileUtil.pm</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./SDFileUtil.html" title="SDFileUtil.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> | <a href="./../pdf/SequenceFileUtil.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/SequenceFileUtil.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/SequenceFileUtil.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/SequenceFileUtil.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<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( + $SequencesDataRef, [$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( + $SequencesDataRef, [$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->{IDs} - Array of sequence IDs +<br/> $SequenceDataMapRef->{Count} - Number of sequences +<br/> $SequenceDataMapRef->{Description}{$ID} - Sequence description +<br/> $SequenceDataMapRef->{Sequence}{$ID} - Sequence for a specific ID +<br/> $SequenceDataMapRef->{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> +<p> </p><p> </p><div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./SDFileUtil.html" title="SDFileUtil.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>