diff mayachemtools/docs/modules/txt/SequenceFileUtil.txt @ 0:73ae111cf86f draft

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+NAME
+    SequenceFileUtil
+
+SYNOPSIS
+    use SequenceFileUtil ;
+
+    use SequenceFileUtil qw(:all);
+
+DESCRIPTION
+    SequenceFileUtil module provides the following functions:
+
+    AreSequenceLengthsIdentical, CalcuatePercentSequenceIdentity,
+    CalculatePercentSequenceIdentityMatrix, GetLongestSequence,
+    GetSequenceLength, GetShortestSequence, IsClustalWSequenceFile,
+    IsGapResidue, IsMSFSequenceFile, IsPIRFastaSequenceFile,
+    IsPearsonFastaSequenceFile, IsSupportedSequenceFile,
+    ReadClustalWSequenceFile, ReadMSFSequenceFile, ReadPIRFastaSequenceFile,
+    ReadPearsonFastaSequenceFile, ReadSequenceFile,
+    RemoveSequenceAlignmentGapColumns, RemoveSequenceGaps,
+    WritePearsonFastaSequenceFile SequenceFileUtil module provides various
+    methods to process sequence files and retreive appropriate information.
+
+FUNCTIONS
+    AreSequenceLengthsIdentical
+            $Status = AreSequenceLengthsIdentical($SequencesDataRef);
+
+        Checks the lengths of all the sequences available in
+        *SequencesDataRef* and returns 1 or 0 based whether lengths of all
+        the sequence is same.
+
+    CalcuatePercentSequenceIdentity
+            $PercentIdentity =
+               AreSequenceLengthsIdenticalAreSequenceLengthsIdentical(
+                  $Sequence1, $Sequence2, [$IgnoreGaps, $Precision]);
+
+        Returns percent identity between *Sequence1* and *Sequence2*.
+        Optional arguments *IgnoreGaps* and *Precision* 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.
+
+    CalculatePercentSequenceIdentityMatrix
+            $IdentityMatrixDataRef = CalculatePercentSequenceIdentityMatrix(
+                                     $SequencesDataRef, [$IgnoreGaps,
+                                     $Precision]);
+
+        Calculate pairwise percent identity between all the sequences
+        available in *SequencesDataRef* and returns a reference to identity
+        matrix hash. Optional arguments *IgnoreGaps* and *Precision* 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.
+
+    GetSequenceLength
+            $SeqquenceLength = GetSequenceLength($Sequence, [$IgnoreGaps]);
+
+        Returns length of the specified sequence. Optional argument
+        *IgnoreGaps* controls handling of gaps. By default, gaps are
+        ignored.
+
+    GetShortestSequence
+           ($ID, $Sequence, $SeqLen, $Description) = GetShortestSequence(
+               $SequencesDataRef, [$IgnoreGaps]);
+
+        Checks the lengths of all the sequences available in
+        $SequencesDataRef and returns $ID, $Sequence, $SeqLen, and
+        $Description values for the shortest sequence. Optional arguments
+        $IgnoreGaps controls handling of gaps in sequences. By default, gaps
+        are ignored.
+
+    GetLongestSequence
+           ($ID, $Sequence, $SeqLen, $Description) = GetLongestSequence(
+               $SequencesDataRef, [$IgnoreGaps]);
+
+        Checks the lengths of all the sequences available in
+        *SequencesDataRef* and returns ID, Sequence, SeqLen, and Description
+        values for the longest sequence. Optional argument $*IgnoreGaps*
+        controls handling of gaps in sequences. By default, gaps are
+        ignored.
+
+    IsGapResidue
+            $Status = AreSequenceLengthsIdentical($Residue);
+
+        Returns 1 or 0 based on whether *Residue* corresponds to a gap. Any
+        character other than A to Z is considered a gap residue.
+
+    IsSupportedSequenceFile
+            $Status = IsSupportedSequenceFile($SequenceFile);
+
+        Returns 1 or 0 based on whether *SequenceFile* corresponds to a
+        supported sequence format.
+
+    IsClustalWSequenceFile
+            $Status = IsClustalWSequenceFile($SequenceFile);
+
+        Returns 1 or 0 based on whether *SequenceFile* corresponds to
+        Clustal sequence alignment format.
+
+    IsPearsonFastaSequenceFile
+            $Status = IsPearsonFastaSequenceFile($SequenceFile);
+
+        Returns 1 or 0 based on whether *SequenceFile* corresponds to
+        Pearson FASTA sequence format.
+
+    IsPIRFastaSequenceFile
+            $Status = IsPIRFastaSequenceFile($SequenceFile);
+
+        Returns 1 or 0 based on whether *SequenceFile* corresponds to PIR
+        FASTA sequence format.
+
+    IsMSFSequenceFile
+            $Status = IsClustalWSequenceFile($SequenceFile);
+
+        Returns 1 or 0 based on whether *SequenceFile* corresponds to MSF
+        sequence alignment format.
+
+    ReadSequenceFile
+            $SequenceDataMapRef = ReadSequenceFile($SequenceFile);
+
+        Reads *SequenceFile* and returns reference to a hash containing
+        following key/value pairs:
+
+            $SequenceDataMapRef->{IDs} - Array of sequence IDs
+            $SequenceDataMapRef->{Count} - Number of sequences
+            $SequenceDataMapRef->{Description}{$ID} - Sequence description
+            $SequenceDataMapRef->{Sequence}{$ID} - Sequence for a specific ID
+            $SequenceDataMapRef->{Sequence}{InputFileType} - File format
+
+    ReadClustalWSequenceFile
+            $SequenceDataMapRef = ReadClustalWSequenceFile($SequenceFile);
+
+        Reads ClustalW *SequenceFile* and returns reference to a hash
+        containing following key/value pairs as describes in
+        ReadSequenceFile method.
+
+    ReadMSFSequenceFile
+            $SequenceDataMapRef = ReadMSFSequenceFile($SequenceFile);
+
+        Reads MSF *SequenceFile* and returns reference to a hash containing
+        following key/value pairs as describes in ReadSequenceFile method.
+
+    ReadPIRFastaSequenceFile
+            $SequenceDataMapRef = ReadPIRFastaSequenceFile($SequenceFile);
+
+        Reads PIR FASTA *SequenceFile* and returns reference to a hash
+        containing following key/value pairs as describes in
+        ReadSequenceFile method.
+
+    ReadPearsonFastaSequenceFile
+            $SequenceDataMapRef = ReadPearsonFastaSequenceFile($SequenceFile);
+
+        Reads Pearson FASTA *SequenceFile* and returns reference to a hash
+        containing following key/value pairs as describes in
+        ReadSequenceFile method.
+
+    RemoveSequenceGaps
+            $SeqWithoutGaps = RemoveSequenceGaps($Sequence);
+
+        Removes gaps from *Sequence* and return a sequence without any gaps.
+
+    RemoveSequenceAlignmentGapColumns
+            $NewAlignmentDataMapRef = RemoveSequenceAlignmentGapColumns(
+                                      $AlignmentDataMapRef);
+
+        Using input alignment data map ref containing following keys,
+        generate a new hash with same set of keys after residue columns
+        containg only gaps have been removed:
+
+            {IDs} : Array of IDs in order as they appear in file
+            {Count}: ID count
+            {Description}{$ID} : Description data
+            {Sequence}{$ID} : Sequence data
+
+    WritePearsonFastaSequenceFile
+            WritePearsonFastaSequenceFile($SequenceFileName, $SequenceDataRef,
+                                          [$MaxLength]);
+
+        Using sequence data specified via *SequenceDataRef*, write out a
+        Pearson FASTA sequence file. Optional argument *MaxLength* controls
+        maximum length sequence in each line; default is 80.
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    PDBFileUtil.pm
+
+COPYRIGHT
+    Copyright (C) 2015 Manish Sud. All rights reserved.
+
+    This file is part of MayaChemTools.
+
+    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.
+