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 <msud@san.rr.com>

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.

