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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

# SEE ALSO

PDBFileUtil.pm

# COPYRIGHT

Copyright (C) 2018 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.

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