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SequenceSimilarityMatrix.pm
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#!/usr/bin/perl
##---------------------------------------------------------------------------##
## File:
## @(#) SequenceSimilarityMatrix.pm
## Author:
## Robert M. Hubley [email protected]
## Description:
## A generic similarity matrix reader
##
#******************************************************************************
#* Copyright (C) 2001 by Robert Hubley, Institute for Systems Biology. *
#* All rights reserved. *
#* *
#* This software is part of a set of software utilities for processing *
#* of genetic sequence data. It should not be redistributed or used for *
#* any commercial purpose, including commercially funded sequencing, *
#* without written permission from the author and the Institute for *
#* Systems Biology. *
#* *
#* This software is provided ``AS IS'' and any express or implied *
#* warranties, including, but not limited to, the implied warranties of *
#* merchantability and fitness for a particular purpose, are disclaimed. *
#* In no event shall the authors or the Institute for Systems Biology be *
#* liable for any direct, indirect, incidental, special, exemplary, or *
#* consequential damages (including, but not limited to, procurement of *
#* substitute goods or services; loss of use, data, or profits; or *
#* business interruption) however caused and on any theory of liability, *
#* whether in contract, strict liability, or tort (including negligence *
#* or otherwise) arising in any way out of the use of this software, even *
#* if advised of the possibility of such damage. *
#* *
#* *
#******************************************************************************
#bless( {
# 'monoAlphabetHash' => {
# 'N' => 1,
# .
# 'G' => 1,
# },
# 'monoSubTotals' => {
# 'G' => '106347',
# .
# 'T' => '183590'
# },
# 'monoSubCounts' => {
# 'GN' => '1',
# .
# 'CT' => '26405'
# },
# 'monoSubProb' => {
# 'TT' => '0.843362928264067',
# .
# 'TC' => '0.074328667138733'
# },
# 'monoSubHash' => {
# 'TT' => '0.91730283955087',
# .
# 'CT' => '0.139273651004344'
# },
# 'monoSubDivergence' => '0.139085568540752',
# 'monoSubScale' => '0.480595582861076',
# 'monoRateHash' => {
# 'TT' => '-0.18872880068887',
# .
# 'CT' => '0.336182624927569'
# },
# 'monoEquilHash' => {
# 'TT' => '0.373615931039398',
# .
# 'CT' => '0.373615931036906'
# },
# 'diSubCounts' => {
# 'GCGG' => '459',
# .
# 'TTCC' => '331'
# },
# 'diEquilHash' => {
# 'CCGT' => '0.0474291179601828',
# .
# 'GCGC' => '0.0189083125022889'
# },
# 'diSubProb' => {
# 'GGCA' => '0.0153687079945481',
# .
# 'CTCG' => '0.00460998830800067'
# },
# 'triSubProb' => {
# 'TAGCGC' => '0.00046029919447641',
# .
# 'AATTCT' => '0.000962721292185912'
# },
# 'trippleSubTotals' => {
# 'AAA' => '30242',
# .
# 'TTT' => '30242'
# },
# 'triSubScale' => '0.359724715125594',
# 'triEquilHash' => {
# 'ACGGGA' => '0.00587170136071818',
# .
# 'AATTCT' => '0.0189427945712668'
# },
# 'triSubDivergence' => '0.138205411835254',
# 'triSubHash' => {
# 'ACGGGA' => '-0.00124954148882776',
# .
# 'AATTCT' => '0.000185848349802029'
# },
# 'trippleAlphabetHash' => {
# 'AAA' => 1,
# .
# 'TTT' => 1
# },
# 'triSubPosCounts' => {
# 'AAA' => {
# '7491' => {
# 'G' => '3',
# 'A' => '204',
# 'C' => '2',
# 'T' => '6'
# },
# '1176' => {
# 'G' => '10',
# 'A' => '237',
# 'C' => '12',
# 'T' => '13'
# }
# 'NAA' => {
# '3097' => {
# 'G' => '19',
# 'A' => '130',
# 'C' => '4',
# 'T' => '18'
# }
# }
# },
# 'triRateHash' => {
# 'ACGGGA' => '-0.0123740187206802',
# .
# 'AATTCT' => '0.000230782000486845'
# },
# 'trippleSubCounts' => {
# 'TAGCGC' => '1',
# .
# 'AATTCT' => '17'
# }
# }, 'SequenceSimilarityMatrix' )
#
###############################################################################
#
# ChangeLog
#
# $Log: SequenceSimilarityMatrix.pm,v $
# Revision 1.22 2017/04/05 00:03:31 rhubley
# Cleanup before a distribution
#
#
###############################################################################
# To Do:
#
#
=head1 NAME
SequenceSimilarityMatrix
=head1 SYNOPSIS
use SequenceSimilarityMatrix;
Usage:
my $matrix = SequenceSimilarityMatrix->new();
=head1 DESCRIPTION
A class for storing a generic sequence similarity
matrix.
=head1 SEE ALSO
=over 4
RepeatModeler
=back
=head1 COPYRIGHT
Copyright 2004 Institute for Systems Biology
=head1 AUTHOR
Robert Hubley <[email protected]>
=head1 INSTANCE METHODS
=cut
package SequenceSimilarityMatrix;
use strict;
use Data::Dumper;
use Carp;
use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS $VERSION);
require Exporter;
@ISA = qw(Exporter);
@EXPORT = qw();
@EXPORT_OK = qw();
%EXPORT_TAGS = ( all => [ @EXPORT_OK ] );
my $CLASS = "SequenceSimilarityMatrix";
##-------------------------------------------------------------------------##
##
##
##-------------------------------------------------------------------------##
sub new
{
my $class = shift;
my $this = {};
bless $this, $class;
return $this;
}
##---------------------------------------------------------------------##
=head2 parseFromFile()
Use: $obj->parseFromFile( "/usr/lib/matrices/blosom64" );
Read a matrix file into the object.
=cut
##---------------------------------------------------------------------##
sub parseFromFile
{
my $object = shift;
my $fileName = shift
|| croak $CLASS. "::parseFromFile() needs a filename!";
open MATRIX, $fileName
or croak "Unable to open matrix file: $fileName : $!";
my %freqHash = ();
my @rowValues = ();
my $row = 0;
my $i = 0;
while ( <MATRIX> )
{
$_ = uc( $_ );
chomp;
if ( /FREQS\s+(.*)/ )
{
%freqHash = split " ", $1;
}
if ( /^\s*[A-Z]\s+[A-Z]\s+[A-Z]\s+[A-Z]\s+/ )
{
chomp;
s/\s//g;
$object->{alphabet} = $_;
$object->{alphabetArray} = [ split( '', $_ ) ];
}
if ( /^\s*([a-zA-Z]\s+)?[\d-]+\s+[\d-]+\s+[\d-]+\s+[\d-]+\s+/ )
{
@rowValues = split;
shift @rowValues if ( $1 ne "" );
my $col = 0;
foreach $a ( @{ $object->{alphabetArray} } )
{
$object->{matrixHash}{ $object->{alphabetArray}[ $row ], $a } =
$rowValues[ $col++ ];
}
$object->{matrix}[ $row++ ] = [ @rowValues ];
}
}
close MATRIX;
if ( scalar( keys %freqHash ) == 0 )
{
$freqHash{"A"} = 0.25;
$freqHash{"C"} = 0.25;
$freqHash{"G"} = 0.25;
$freqHash{"T"} = 0.25;
}
for ( $i = 0 ; $i < length( $object->{alphabet} ) ; $i++ )
{
$object->{freqArray}[ $i ] =
$freqHash{ substr( $object->{alphabet}, $i, 1 ) } || 0;
}
}
##-------------------------------------------------------------------------##
## Serialization & Debug Routines
##-------------------------------------------------------------------------##
##-------------------------------------------------------------------------##
## Use: toString([$object]);
##
## $object : Normally passed implicitly
##
## Returns
##
## Uses the Data::Dumper to create a printable reprentation
## of a data structure. In this case the object data itself.
##
##-------------------------------------------------------------------------##
## TODO: This could be moved into a generic object class.
## or placed in perlhelpers module.
sub toString
{
my $object = shift;
my $data_dumper = new Data::Dumper( [ $object ] );
$data_dumper->Purity( 1 )->Terse( 1 )->Deepcopy( 1 );
return $data_dumper->Dump();
}
##-------------------------------------------------------------------------##
## Use: my serializeOUT( $filename );
##
## $filename : A filename to be created
##
## Returns
##
## Uses the Data::Dumper module to save out the data
## structure as a text file. This text file can be
## read back into an object of this type.
##
##-------------------------------------------------------------------------##
sub serializeOUT
{
my $object = shift;
my $fileName = shift;
my $data_dumper = new Data::Dumper( [ $object ] );
$data_dumper->Purity( 1 )->Terse( 1 )->Deepcopy( 1 );
open OUT, ">$fileName";
print OUT $data_dumper->Dump();
close OUT;
}
##-------------------------------------------------------------------------##
## Use: my serializeIN( $filename );
##
## $filename : A filename containing a serialized object
##
## Returns
##
## Uses the Data::Dumper module to read in data
## from a serialized PERL object or data structure.
##
##-------------------------------------------------------------------------##
sub serializeIN
{
my $object = shift;
my $fileName = shift;
my $fileContents = "";
my $oldSep = $/;
undef $/;
my $in;
open $in, "$fileName";
$fileContents = <$in>;
$/ = $oldSep;
close $in;
return eval( $fileContents );
}
##-------------------------------------------------------------------------##
=head2 addMatrices()
Use: my addMatrices( $matrixObject,
$addCounts,
$addRates,
$addSubs );
$matrixObject : Add the counts (and alphabet) from
$matrixObject to this one.
$addCounts : Boolean. Add mono/tri counts.
$addRates : Boolean. Add mono/tri rates.
$addSubs : Boolean. Add mono/tri substitution values.
Modifies the object by adding the data from another
matrix object to this one. NOTE: It also adds to the
alphabet if necessary.
=cut
##-------------------------------------------------------------------------##
sub addMatrices
{
my $object = shift;
my $matrix = shift;
my $addCounts = shift;
my $addRates = shift;
my $addSubs = shift;
# Mono nucleotide counts
foreach my $cBase ( keys( %{ $matrix->{monoAlphabetHash} } ) )
{
# Add to alphabets if necessary
$object->{monoAlphabetHash}{$cBase} = 1;
# Add matrix counts to object counts
foreach my $sBase ( keys( %{ $matrix->{monoAlphabetHash} } ) )
{
$object->{monoSubCounts}{ $cBase . $sBase } +=
$matrix->{monoSubCounts}{ $cBase . $sBase }
if ( $addCounts && $matrix->{monoSubCounts}{ $cBase . $sBase } > 0 );
$object->{monoRateHash}{ $cBase . $sBase } +=
$matrix->{monoRateHash}{ $cBase . $sBase }
if ( $addRates && $matrix->{monoRateHash}{ $cBase . $sBase } > 0 );
$object->{monoSubHash}{ $cBase . $sBase } +=
$matrix->{monoSubHash}{ $cBase . $sBase }
if ( $addSubs && $matrix->{monoSubHash}{ $cBase . $sBase } > 0 );
}
}
# Tri nucleotide counts
foreach my $cBase ( keys( %{ $matrix->{trippleAlphabetHash} } ) )
{
# Add to alphabets if necessary
$object->{trippleAlphabetHash}{$cBase} = 1;
# Add matrix counts to object counts
foreach my $sBase ( keys( %{ $matrix->{trippleAlphabetHash} } ) )
{
$object->{trippleSubCounts}{ $cBase . $sBase } +=
$matrix->{trippleSubCounts}{ $cBase . $sBase }
if ( $addCounts
&& $matrix->{trippleSubCounts}{ $cBase . $sBase } > 0 );
$object->{triRateHash}{ $cBase . $sBase } +=
$matrix->{triRateHash}{ $cBase . $sBase }
if ( $addRates && $matrix->{triRateHash}{ $cBase . $sBase } > 0 );
$object->{triSubHash}{ $cBase . $sBase } +=
$matrix->{triSubHash}{ $cBase . $sBase }
if ( $addSubs && $matrix->{triSubHash}{ $cBase . $sBase } > 0 );
}
}
}
##-------------------------------------------------------------------------##
=head2 div()
Use: my div($value,
$counts,
$rates,
$subs );
$value : The value to divide the matrix by
$counts : Boolean. divide mono/tri counts by value.
$rates : Boolean. divide mono/tri rates by value.
$subs : Boolean. divide mono/tri substitution by value.
Modifies the object by dividing the matrix by a constant
value.
=cut
##-------------------------------------------------------------------------##
sub divMatrices
{
my $object = shift;
my $value = shift;
my $counts = shift;
my $rates = shift;
my $subs = shift;
# Mono nucleotide matrices
foreach my $cBase ( keys( %{ $object->{monoAlphabetHash} } ) )
{
foreach my $sBase ( keys( %{ $object->{monoAlphabetHash} } ) )
{
$object->{monoSubCounts}{ $cBase . $sBase } /= $value
if ( $counts && $object->{monoSubCounts}{ $cBase . $sBase } > 0 );
$object->{monoRateHash}{ $cBase . $sBase } /= $value
if ( $rates && $object->{monoRateHash}{ $cBase . $sBase } > 0 );
$object->{monoSubHash}{ $cBase . $sBase } /= $value
if ( $subs && $object->{monoSubHash}{ $cBase . $sBase } > 0 );
}
}
# Tri nucleotide matrices
foreach my $cBase ( keys( %{ $object->{trippleAlphabetHash} } ) )
{
foreach my $sBase ( keys( %{ $object->{trippleAlphabetHash} } ) )
{
$object->{trippleSubCounts}{ $cBase . $sBase } /= $value
if ( $counts && $object->{trippleSubCounts}{ $cBase . $sBase } > 0 );
$object->{triRateHash}{ $cBase . $sBase } /= $value
if ( $rates && $object->{triRateHash}{ $cBase . $sBase } > 0 );
$object->{triSubHash}{ $cBase . $sBase } /= $value
if ( $subs && $object->{triSubHash}{ $cBase . $sBase } > 0 );
}
}
}
##-------------------------------------------------------------------------##
## Use: my $divergence = _matrixDivergence( \@matrixArrayRef,
## $alphabetRef,
## [$monoFreqHashRef] );
##
## \@matrixArrayRef : A square probability matrix
## $AlphabetArrayRef : Array header
## $monoFreqHashRef : A hash of mono nucleotides and
## their frequencies within the
## background for which this matrix
## is tuned.
##
## Returns
##
## Performs one of two types of divergence calculations
## based on the presence of mono-nucleotide background
## frequencies.
##
## If frequencies are not present it calculates the
## divergence as the inverse of the average diagonal
## probability.
##
## If the frequences are present it calculates the
## divergence as the inverse of the sum of weighted
## probabilities. ie.
##
## 1 - ( p(A)*p(A->A) + p(C) * p(C->C)...)
##
##-------------------------------------------------------------------------##
sub _matrixDivergence
{
my $matrixArrayRef = shift;
my $alphabetArrayRef = shift;
my $monoFreqHashRef = shift;
my $diagTotal = 0;
for ( my $i = 0 ; $i <= $#$matrixArrayRef ; $i++ )
{
if ( defined $monoFreqHashRef )
{
$diagTotal +=
$matrixArrayRef->[ $i ][ $i ] *
$monoFreqHashRef->{ $alphabetArrayRef->[ $i ] };
} else
{
$diagTotal += $matrixArrayRef->[ $i ][ $i ];
}
}
if ( defined $monoFreqHashRef )
{
return ( 1 - ( $diagTotal ) );
} else
{
return ( 1 - ( $diagTotal / ( $#$matrixArrayRef + 1 ) ) );
}
}
##-------------------------------------------------------------------------##
## Use: my $divergence = _triMatrixDivergence( $matrixArrayRef
## $alphabetArrayRef,
## [$noCGSites],
## [$trippletFreqHashRef]);
##
## $matrixArrayRef : A square probability matrix
## $alphabetArrayRef : The row/column identifiers
## $noCGSites : Optional parameter to ignore
## sites containing CGs.
## $trippletFreqHashRef : Optional parameter to use
## tripplet backgound frequencies to
## weight the calculation.
##
## Returns
##
## Performs one of several types of divergence calculations
## based on the presence of tri-nucleotide background
## frequencies (trippletFreqHashRef), and or the flag
## $noCGSites.
##
## The basic divergence calculation (when neither $noCGSites
## or $trippletFreqHashRef are set/defined) is defined as
## the inverse average of all loose-perfect probabilities.
## Ie.
## 1 - Avg(p(AAA->NAN) + p(AAT->NAN) + p(AAC->NAN) +....)
##
## The $noCGSites option simply removed all p(NCG->NCN) and
## p(CGN->NGN) terms from the previous calculation.
##
## If $trippletFreqHashRef is defined a very different
## formula is used. NOTE: That the $noCGSites option
## can also be used with this formula but may not
## make much sense:
##
## 1 - (p(AAA) * p(AAA->NAN) + p(AAT) * p(AAT->NAN) + ....)
##
##-------------------------------------------------------------------------##
sub _triMatrixDivergence
{
my $matrixArrayRef = shift;
my $alphabetArrayRef = shift;
my $noCGSites = shift;
my $trippletFreqHashRef = shift;
my $diagTotal = 0;
my $diagElements = 0;
for ( my $i = 0 ; $i <= $#$matrixArrayRef ; $i++ )
{
next if ( $noCGSites && index( $alphabetArrayRef->[ $i ], "CG" ) >= 0 );
$diagElements++;
for ( my $j = 0 ; $j <= $#$matrixArrayRef ; $j++ )
{
if (
substr( $alphabetArrayRef->[ $i ], 1, 1 ) eq
substr( $alphabetArrayRef->[ $j ], 1, 1 ) )
{
if ( defined $trippletFreqHashRef )
{
$diagTotal +=
( $matrixArrayRef->[ $i ][ $j ] *
$trippletFreqHashRef->{ $alphabetArrayRef->[ $i ] } );
} else
{
$diagTotal += $matrixArrayRef->[ $i ][ $j ];
}
}
}
}
if ( defined $trippletFreqHashRef )
{
return ( 1 - ( $diagTotal ) );
} else
{
return ( 1 - ( $diagTotal / $diagElements ) );
}
}
sub hashToArray
{
my $object = shift;
my $matrixHashRef = shift;
my $alphabetArrayRefOrig = shift;
my ( @matrixArray, $alphabetArrayRef ) =
_hashToArray( $matrixHashRef, $alphabetArrayRefOrig );
return ( \@matrixArray, $alphabetArrayRef );
}
##-------------------------------------------------------------------------##
## Use: my \@matrixArray = _hashToArray( \%matrixHashRef,
## [$alphabetArrayRef] );
##
## \%matrixHashRef : A hash which contains array information
## stored as two concatenated equal length
## keys. ie.
##
## A B %matrixHash{AA} = 0
## A 0 1 %matrixHash{AB} = 1
## B 1 0 %matrixHash{BA} = 1
## %matrixHash{BB} = 0
##
## $alphabetArrayRef : Optional. Instead of using the
## the keys from the hash to determine
## the matrix dimensions...use this
## array as key pairs in the hash.
##
## Returns
##
## A PERL array form of the hash matrix data.
##
##-------------------------------------------------------------------------##
sub _hashToArray
{
my $matrixHashRef = shift;
my $alphabetArrayRef = shift;
# Calculate the unique set of key pairs for the
# hash if we are not given this information already
unless ( defined $alphabetArrayRef )
{
my %seen = ();
$alphabetArrayRef = [
grep { !$seen{$_}++ }
map {
(
substr( $_, 0, length( $_ ) / 2 ),
substr( $_, length( $_ ) / 2, length( $_ ) / 2 )
)
}
keys( %{$matrixHashRef} )
];
}
# Build the array.
my $i = 0;
my $j = 0;
my @matrixArray = ();
foreach my $conSeq ( @{$alphabetArrayRef} )
{
foreach my $subSeq ( @{$alphabetArrayRef} )
{
$matrixArray[ $i ][ $j++ ] = $matrixHashRef->{ $conSeq . $subSeq };
}
$j = 0;
$i++;
}
return ( \@matrixArray, $alphabetArrayRef );
}
##-------------------------------------------------------------------------##
## Use: my \%matrixHash = _arrayToHash( \@matrixArrayRef,
## \@alphabetArrayRef );
##
## \@matrixArrayef : An square array
## \@alphabetArrayRef : The col/row identifiers to be
## used as keys in the hash.
##
## ie.
##
## A B %matrixHash{AA} = 0
## A 0 1 %matrixHash{AB} = 1
## B 1 0 %matrixHash{BA} = 1
## %matrixHash{BB} = 0
##
## Returns
##
## A PERL hash form of the array matrix data.
##
##-------------------------------------------------------------------------##
sub _arrayToHash
{
my $matrixArrayRef = shift;
my $alphabetArrayRef = shift;
# Build the hash.
my $i = 0;
my $j = 0;
my %matrixHash = ();
foreach my $conSeq ( @{$alphabetArrayRef} )
{
foreach my $subSeq ( @{$alphabetArrayRef} )
{
$matrixHash{ $conSeq . $subSeq } = $matrixArrayRef->[ $i ][ $j++ ];
}
$j = 0;
$i++;
}
return ( \%matrixHash );
}
##-------------------------------------------------------------------------##
=head2 matrixToString()
TODO: DOCUMENT!
=cut
##-------------------------------------------------------------------------##
sub matrixToString
{
my $object = shift;
my $name = shift;
my $compressed = shift;
my $excludeNs = shift;
return _matrixHashToString( $object->{$name}, $compressed, $excludeNs );
}
##-------------------------------------------------------------------------##
=head2 triStandardDeviation()
TODO: DOCUMENT!
=cut
##-------------------------------------------------------------------------##
sub triStandardDeviation
{
my $object = shift;
my $outStr = "";
my %seen = ();
my @alphabet = grep { !$seen{$_}++; }
map { ( substr( $_, 0, 3 ), substr( $_, 3 ) ); }
keys( %{ $object->{trippleSubCounts} } );
%seen = ();
my @sortedMidAlphabet =
( sort grep { !$seen{$_}++; }
( map { ( substr( $_, 1, 1 ) ); } @alphabet ) );
my @sortedAlphabet = (
sort {
substr( $a, 1, 1 ) cmp substr( $b, 1, 1 )
|| substr( $a, 0, 1 ) cmp substr( $b, 0, 1 )
|| substr( $a, 2, 1 ) cmp substr( $b, 2, 1 )
} @alphabet
);
$outStr .= "Tripplet Position Standard Deviation\n";
$outStr .= "====================================\n";
$outStr .= "\t";
foreach my $tripplet ( ( "A", "C", "G", "T" ) )
{
$outStr .= "$tripplet\t";
}
$outStr .= "\n";
foreach my $tripplet ( @sortedAlphabet )
{
next if ( ( $tripplet =~ /N/ ) );
my %triBaseTotals = ();
my $numOfPositionsInSeq = 0;
my %meanBaseCount = ();
my %sumOfSquaredDistance = ();
foreach my $pos ( keys( %{ $object->{triSubPosCounts}{$tripplet} } ) )
{
$numOfPositionsInSeq++;
foreach
my $sub ( keys( %{ $object->{triSubPosCounts}{$tripplet}{$pos} } ) )
{
next if ( $sub eq "N" );
$triBaseTotals{$sub} +=
$object->{triSubPosCounts}{$tripplet}{$pos}{$sub};
$meanBaseCount{$sub} = $triBaseTotals{$sub} / $numOfPositionsInSeq++;
}
}
foreach my $pos ( keys( %{ $object->{triSubPosCounts}{$tripplet} } ) )
{
foreach
my $sub ( keys( %{ $object->{triSubPosCounts}{$tripplet}{$pos} } ) )
{
next if ( $sub eq "N" );
$sumOfSquaredDistance{$sub} +=
( $object->{triSubPosCounts}{$tripplet}{$pos}{$sub} -
$meanBaseCount{$sub} )**2;
}
}
$outStr .= "$tripplet\t";
foreach my $sub ( sort keys( %sumOfSquaredDistance ) )
{
$object->{sdTriBaseCounts}{$tripplet}{$sub} +=
sqrt(
( 1 / ( $numOfPositionsInSeq - 1 ) ) * $sumOfSquaredDistance{$sub} );
$outStr .=
sprintf( "%0.6g", $object->{sdTriBaseCounts}{$tripplet}{$sub} )
. "\t";
}
$outStr .= "\n";
}
return ( $outStr );
}
##-------------------------------------------------------------------------##
##
##
##-------------------------------------------------------------------------##
sub _matrixHashToString
{
my $matrixHashRef = shift;
my $compressed = shift;
my $excludeNs = shift;
my $outStr = "";
#
# Sort the matrix col/row headings (alphabet)
#
my @sortedAlphabet = ();
my @sortedMidAlphabet = ();
my @alphabet = ();
my %seen = ();
my $keyLen = length( ( keys( %{$matrixHashRef} ) )[ 0 ] );
if ( $excludeNs )
{
@alphabet = grep { !$seen{$_}++ && !/N/; }
map { ( substr( $_, 0, $keyLen / 2 ), substr( $_, $keyLen / 2 ) ); }
keys( %{$matrixHashRef} );
} else
{
@alphabet = grep { !$seen{$_}++; }
map { ( substr( $_, 0, $keyLen / 2 ), substr( $_, $keyLen / 2 ) ); }
keys( %{$matrixHashRef} );
}
if ( $keyLen == 6 )
{
my %seen = ();
@sortedMidAlphabet =
( sort grep { !$seen{$_}++; }
( map { ( substr( $_, 1, 1 ) ); } @alphabet ) );
@sortedAlphabet = (
sort {
substr( $a, 1, 1 ) cmp substr( $b, 1, 1 )
|| substr( $a, 0, 1 ) cmp substr( $b, 0, 1 )
|| substr( $a, 2, 1 ) cmp substr( $b, 2, 1 )
} @alphabet
);
} else
{
@sortedAlphabet = ( sort( @alphabet ) );
}
#
# Form the report string
#
$outStr .= "\t";
my $colIndex = "";
my %colTot = ();
# Generate the column headings
if ( $compressed )
{
foreach $colIndex ( @sortedMidAlphabet )
{
$outStr .= "$colIndex\t";
}
} else
{
foreach $colIndex ( @sortedAlphabet )
{
$outStr .= "$colIndex\t";
}
}
$outStr .= "\n";
# Generate the rows
my $rowIndex = "";
foreach $rowIndex ( @sortedAlphabet )
{
$outStr .= "$rowIndex\t";
foreach $colIndex ( @sortedAlphabet )
{
if ( $compressed )
{
$colTot{ substr( $colIndex, 1, 1 ) } +=
$matrixHashRef->{ $rowIndex . $colIndex };
} else
{
$outStr .= ""
. sprintf( "%.6g", $matrixHashRef->{ $rowIndex . $colIndex } )
. "\t";
}
}
if ( $compressed )
{
map { $outStr .= sprintf( "%.6g", $colTot{$_} ) . "\t"; }
@sortedMidAlphabet;
%colTot = undef;
}
$outStr .= "\n";
}
$outStr .= "\n\n";
return ( $outStr );
}
##-------------------------------------------------------------------------##
=head2 calculateLLRMatrices()
TODO: DOCUMENT!
=cut
##-------------------------------------------------------------------------##
sub calculateLLRMatrices
{
my $object = shift;
my $backgroundGC = shift;
my $scale = shift;
my $outStr = "FREQS A "
. ( ( 1 - $backgroundGC ) / 2 ) . " C "
. ( $backgroundGC / 2 ) . " G "
. ( $backgroundGC / 2 ) . " T "
. ( ( 1 - $backgroundGC ) / 2 ) . "\n";
$outStr .= "A\tR\tG\tC\tY\tT\tK\tM\tS\tW\tN\tX\n";
#
# Create a IUB Matrix and a background vector
#
my @cBaseArray = ();
my @sBaseArray = ();
foreach my $cBase ( "A", "R", "G", "C", "Y", "T", "K", "M", "S", "W" )
{
if ( $cBase eq "A" || $cBase eq "T" || $cBase eq "G" || $cBase eq "C" )
{
@cBaseArray = ( $cBase );
} elsif ( $cBase eq "R" )
{
# A or G (Purines)
@cBaseArray = ( "A", "G" );
} elsif ( $cBase eq "Y" )