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WUBlastXSearchEngine.pm
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WUBlastXSearchEngine.pm
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#!/usr/bin/perl -w
##---------------------------------------------------------------------------##
## File:
## @(#) WUBlastXSearchEngine.pm
## Author:
## Robert M. Hubley [email protected]
## Description:
## An implementation of SearchEngineI for the
## the WU-BlastX search engine.
##
#******************************************************************************
#* Copyright (C) Institute for Systems Biology 2003-2004 Developed by
#* Arian Smit and Robert Hubley.
#*
#* This work is licensed under the Open Source License v2.1. To view a copy
#* of this license, visit http://www.opensource.org/licenses/osl-2.1.php or
#* see the license.txt file contained in this distribution.
#*
#******************************************************************************
# Implementation Details:
#
# bless(
# 'WUBlastXSearchEngine' );
#
###############################################################################
# ChangeLog
#
# $Log$
#
###############################################################################
# To Do:
#
#
=head1 NAME
WUBlastXSearchEngine
=head1 SYNOPSIS
use WUBlastXSearchEngine
Usage:
use SearchEngineI;
use WUBlastXSearchEngine;
use SearchResultCollection;
my $wuEngine = WUBlastXSearchEngine->new(
pathToEngine=>"/usr/local/wublast/blastx" );
$wuEngine->setMatrix( "/users/bob/simple.matrix" );
$wuEngine->setQuery( "/users/bob/query.fasta" );
$wuEngine->setSubject( "/users/bob/subject.fasta" );
my $searchResults = $wuEngine->search();
=head1 DESCRIPTION
A concrete implementation of the abstract class / interface SearchEngineI
which use the WUBlastX sequence search engine.
=head1 INSTANCE METHODS
=cut
package WUBlastXSearchEngine;
use strict;
use SearchEngineI;
use SearchResultCollection;
use Data::Dumper;
use FileHandle;
use File::Basename;
use Carp;
use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS $VERSION);
require Exporter;
@ISA = qw(Exporter SearchEngineI);
@EXPORT = qw();
@EXPORT_OK = qw();
%EXPORT_TAGS = ( all => [ @EXPORT_OK ] );
#
# Constants
#
use constant Query => 1;
use constant Subject => 2;
#
# Version
#
my $VERSION = 0.1;
my $CLASS = "WUBlastXSearchEngine";
my $DEBUG = 0;
##-------------------------------------------------------------------------##
## Constructor
##-------------------------------------------------------------------------##
sub new {
my $class = shift;
my %nameValuePairs = @_;
croak $CLASS
. "::new: Missing path to search engine!\n\n"
. "use \$searchEngine = $CLASS->new( pathToEngine=>\"/usr/local/"
. "bin/blastp\")\n"
if ( not defined $nameValuePairs{'pathToEngine'} );
# Create ourself as a hash
my $this = {};
# Bless this hash in the name of the father, the son...
bless $this, $class;
$this->setPathToEngine( $nameValuePairs{'pathToEngine'} );
return $this;
}
##-------------------------------------------------------------------------##
## Get and Set Methods
##-------------------------------------------------------------------------##
##-------------------------------------------------------------------------##
=head2 get_setOverrideParameters()
Use: my $value = getOverrideParameters( );
Use: my $oldValue = setOverrideParameters( $value );
Get/Set the the override paramters. These are used instead
of all the SearchEngineI default parameters if set.
=cut
##-------------------------------------------------------------------------##
sub getOverrideParameters {
my $this = shift;
return $this->{'overrideParameters'};
}
sub setOverrideParameters {
my $this = shift;
my $value = shift;
my $oldValue = $this->{'overrideParameters'};
$this->{'overrideParameters'} = $value;
return $oldValue;
}
##-------------------------------------------------------------------------##
=head2 MaskLevelSequence()
Use: my $value = getMaskLevelSequence( );
Use: my $oldValue = setMaskLevelSequence( $value );
Get/Set the MaskLevelSequence paramter. This is the
sequence ( SearchResult::Query or SearchResult::Subject )
which will be considered when applying the mask level. The
default is SearchResult::Query.
=cut
##-------------------------------------------------------------------------##
sub getMaskLevelSequence {
my $this = shift;
return $this->{'maskLevelSequence'};
}
sub setMaskLevelSequence {
my $this = shift;
my $value = shift;
croak $CLASS
. "::setMaskLevelSequence: Invalid value ( $value ). "
. "Should be either SearchResult::Query or "
. "SearchResult::Subject\n"
if ( $value != SearchResult::Query
&& $value != SearchResult::Subject );
my $oldValue = $this->{'maskLevelSequence'};
$this->{'maskLevelSequence'} = $value;
return $oldValue;
}
##-------------------------------------------------------------------------##
=head2 PValueCutoff()
Use: my $value = getPValueCutoff( );
Use: my $oldValue = setPValueCutoff( $value );
Get/Set the PValueCutoff.
=cut
##-------------------------------------------------------------------------##
sub getPValueCutoff {
my $this = shift;
return $this->{'PValueCutoff'};
}
sub setPValueCutoff {
my $this = shift;
my $value = shift;
my $oldValue = $this->{'PValueCutoff'};
$this->{'PValueCutoff'} = $value;
return $oldValue;
}
##-------------------------------------------------------------------------##
=head2 FilterWords()
Use: my $value = getFilterWords( );
Use: my $oldValue = setFilterWords( $value );
Turn on / off the Dust/Seg/Xnu screening of words.
=cut
##-------------------------------------------------------------------------##
sub getFilterWords {
my $this = shift;
return $this->{'filterWords'};
}
sub setFilterWords {
my $this = shift;
my $value = shift;
my $oldValue = $this->{'filterWords'};
$this->{'filterWords'} = $value;
return $oldValue;
}
##-------------------------------------------------------------------------##
=head2 TempDir()
Use: my $value = getTempDir( );
Use: my $oldValue = setTempDir( $value );
Set the directory to use as a temp directory for a search.
The default is to use the directory which contains the query sequence.
=cut
##-------------------------------------------------------------------------##
sub getTempDir {
my $this = shift;
return $this->{'tempDir'};
}
sub setTempDir {
my $this = shift;
my $value = shift;
my $oldValue = $this->{'tempDir'};
$this->{'tempDir'} = $value;
return $oldValue;
}
##-------------------------------------------------------------------------##
=head2 get_setAdditionalParameters()
Use: my $value = getAdditionalParameters( );
Use: my $oldValue = setAdditionalParameters( $value );
Get/Set the additional paramters. These are used in addition
to the existing parameter set.
=cut
##-------------------------------------------------------------------------##
sub getAdditionalParameters {
my $this = shift;
return $this->{'additionalParameters'};
}
sub setAdditionalParameters {
my $this = shift;
my $value = shift;
my $oldValue = $this->{'additionalParameters'};
$this->{'additionalParameters'} = $value;
return $oldValue;
}
##-------------------------------------------------------------------------##
=head2 get_setPathToEngine()
Use: my $value = getPathToEngine( );
Use: my $oldValue = setPathToEngine( $value );
Get/Set the fully qualified path to the search engine
binary file.
=cut
##-------------------------------------------------------------------------##
sub getPathToEngine {
my $this = shift;
return $this->{'pathToEngine'};
}
sub setPathToEngine {
my $this = shift;
my $value = shift;
croak $CLASS. "::setPathToEngine( $value ): Program does not exist!"
if ( not -x $value || `which $value` );
my $result = `$value 2>&1`;
if ( $result =~ /^(BLASTX) (\S+ \[.*\])/m ) {
$this->{'version'} = $2;
$this->{'engineName'} = $1;
}
else {
croak $CLASS
. "::setPathToEngine( $value ): Cannot determine "
. "engine variant and version!\n";
}
my $oldValue = $this->{'pathToEngine'};
$this->{'pathToEngine'} = $value;
return $oldValue;
}
##-------------------------------------------------------------------------##
## Instance Methods
##-------------------------------------------------------------------------##
##-------------------------------------------------------------------------##
=head2 search()
Use: my ( $resultCode, $SearchResultCollectionI ) = search( );
or
Use: my ( $resultCode, $SearchResultCollectionI )
= search( matrix=>"7p16g.matrix",
...
);
Run the search and return a SearchResultCollection.
=cut
##-------------------------------------------------------------------------##
sub search {
my $this = shift;
my %nameValuePairs = @_;
if ( %nameValuePairs ) {
while ( my ( $name, $value ) = each( %nameValuePairs ) ) {
my $method = "set" . _ucFirst( $name );
unless ( $this->can( $method ) ) {
croak( $CLASS . "::search: Instance variable $name doesn't exist." );
}
$this->$method( $value );
}
}
# Test if engine is available
my $engine = $this->getPathToEngine();
if ( !defined $engine || !-f "$engine" ) {
croak $CLASS
. "::search: The path to the search engine is undefined or\n"
. "is set incorrectly: $engine\n";
}
# Generate parameter line
my $parameters = "";
my $spanParameter = "";
my $value;
if ( ( $value = $this->getSubject() ) ) {
# Make sure we have the compressed form of the database handy
if ( -f "$value.ahd" || -f "$value.xns" || -f "$value.xps" ) {
$parameters .= " $value";
}
else {
croak $CLASS
. "::search: Error...compressed subject "
. "database ($value) does not exist!\n";
}
}
else {
croak $CLASS. "::search: Error subject undefined!\n";
}
my $outputDirName;
if ( ( $value = $this->getQuery() ) ) {
if ( -f $value ) {
$parameters .= " $value";
}
else {
croak $CLASS. "::search: Error...query ($value) does not exist!\n";
}
if ( defined $this->getTempDir() && -d $this->getTempDir() ) {
$outputDirName = $this->getTempDir();
}
else {
$outputDirName = dirname( $value );
}
}
else {
croak $CLASS. "::search: Error query undefined!\n";
}
# Constant parameters
$parameters .= " -warnings -T=1000000 hspmax=2000000000 B=100000000";
if ( $this->{'filterWords'} >= 1 ) {
$parameters .= " wordmask=xnu";
}
if ( defined( $value = $this->getGapInit() )
&& $value =~ /\d+/ )
{
$parameters .= " Q=" . abs( $value );
}
if ( defined( $value = $this->getInsGapExt() )
&& $value =~ /\d+/ )
{
$parameters .= " R=" . abs( $value );
}
if ( defined( $value = $this->getMinMatch() )
&& $value =~ /\d+/ )
{
$parameters .= " W=$value";
}
# S: Overall score threshold...not sure how this relates to the others
# S2: Score threshold for ungapped HSPs
# gapS2: Score threshold for gapped HSPs
# X: Dropoff score for ungapped HSPs
# gapX: Dropoff score for gapped HSPs
# if ( defined( $value = $this->getMinScore() )
# && $value =~ /\d+/ )
# {
# $parameters .= " S=$value";
# $parameters .= " gapS2=$value";
# $parameters .= " S2=" . int( $value / 2 );
# $parameters .= " X=$value";
# $parameters .= " gapX=" . ( $value * 2 );
# }
if ( defined( $value = $this->getBandwidth() )
&& $value =~ /\d+/ )
{
$parameters .= " gapW=" . ( ( $value * 3 ) + 1 );
}
if ( defined( $value = $this->getMatrix() ) ) {
# Test if matrix exists
if ( -f $value ) {
# WUBLAST requires that the matrix filename parameter
# be relative to a directory path specified in
# environment variables.
my @path = split( /[\\\/]/, $value );
my $matrix = pop @path;
# WUBLAST expects the path to be above "aa" or "nt" sub
# directories
if ( $path[ $#path ] eq "aa" || $path[ $#path ] eq "nt" ) {
pop @path;
}
# Set the environment
$ENV{BLASTMAT} = join( "/", @path );
$ENV{WUBLASTMAT} = $ENV{BLASTMAT};
$parameters .= " -matrix=$matrix";
}
else {
croak $CLASS. "::search: Error...matrix ($value) does not exist!\n";
}
}
# Invoke engine and handle errors
my $POUTPUT = new FileHandle;
my $errFile;
do {
$errFile = $outputDirName . "/wuResults-" . time() . ".err";
} while ( -f $errFile );
my $pid;
my $runParameters;
if ( defined $this->{'overrideParameters'}
&& $this->{'overrideParameters'} ne "" )
{
$runParameters = $this->{'overrideParameters'};
}
else {
$runParameters = $parameters . " ";
}
if ( defined $this->{'additionalParameters'}
&& $this->{'additionalParameters'} ne "" )
{
$runParameters .= " " . $this->{'additionalParameters'};
}
print $CLASS
. "::search() Invoking search engine as: $engine "
. "$runParameters 2>$errFile |\n"
if ( $DEBUG );
$pid = open( $POUTPUT, "$engine $runParameters 2>$errFile |" );
# Create SearchResultCollection object from
# the engine results.
my $searchResultsCollection;
if ( $DEBUG ) {
## Create a debug file
my $outFile;
do {
$outFile = $outputDirName . "/wuResults-" . time() . ".out";
} while ( -f $outFile );
open OUT, ">$outFile";
while ( <$POUTPUT> ) {
print OUT $_;
}
close OUT;
close $POUTPUT;
$searchResultsCollection = parseOutput(
searchOutput => $outFile,
pValueCutoff => $this->getPValueCutoff(),
scoreMode => $this->getScoreMode(),
scoreCutoff => $this->getMinScore()
);
}
else {
# Just pipe to the parser
$searchResultsCollection = parseOutput(
searchOutput => $POUTPUT,
pValueCutoff => $this->getPValueCutoff(),
scoreMode => $this->getScoreMode(),
scoreCutoff => $this->getMinScore()
);
}
close $POUTPUT;
my $resultCode = ( $? >> 8 );
print "WUBlast returned a the following result code >$resultCode<\n"
if ( $DEBUG );
# This result code can occur if wublast encounters a sequence
# (at the end of a query collection) which is short enough
# that it would never score higher than the threshold. An
# exit code of 16 | 17 occurs with a printed error of
# "FATAL: There are no valid contexts in the requested search."
# Look for this and ignore. NOTE: In WUBLast 2.0 ( non free version )
# you can use the -novalidctxok option to warn but not return a bad exit
# code.
if ( $resultCode != 0 ) {
open ERR, "<$errFile";
my $errOk = 1;
while ( <ERR> ) {
if ( /^FATAL:/ ) {
if ( !/context|cpus|P option|uses P|shorter/i ) {
$errOk = 0;
print STDERR $CLASS . "::search: $_\n";
}
}
}
close ERR;
$resultCode = 0 if ( $errOk == 1 );
}
unlink $errFile unless ( $DEBUG );
print $CLASS
. "::search: "
. $searchResultsCollection->size()
. " hits " . "\n"
if ( $DEBUG );
#
# Postprocess the results
#
if ( defined $searchResultsCollection
&& $searchResultsCollection->size() > 0 )
{
#
# Mask level filtering
#
my $maskLevel;
my $strand;
if ( defined( $maskLevel = $this->getMaskLevel() ) ) {
if ( defined( $strand = $this->getMaskLevelSequence() ) ) {
$searchResultsCollection->maskLevelFilter( value => $maskLevel,
strand => $strand );
}
else {
$searchResultsCollection->maskLevelFilter( value => $maskLevel );
}
print $CLASS
. "::search: "
. $searchResultsCollection->size()
. " hits "
. "after masklevel filtering\n"
if ( $DEBUG );
}
# Secondary sort by query position
$searchResultsCollection->sort(
sub ($$) {
$_[ 0 ]->getQueryName cmp $_[ 1 ]->getQueryName()
|| $_[ 0 ]->getQueryStart() <=> $_[ 1 ]->getQueryStart();
}
);
}
return ( $resultCode, $searchResultsCollection );
}
##-------------------------------------------------------------------------##
=head1 Class Methods
=cut
##-------------------------------------------------------------------------##
##---------------------------------------------------------------------##
=head2 parseOutput()
Use: my \@results = &parseWublastXOutput( searchOutput => "",
pValueCutoff => #,
scoreMode => "",
scoreCutoff => #
);
searchOutput : WublastX results file or FH
pValueCutoff : Lowest pValue to include in results
Returns
A SearchResultCollection with all the results.
=cut
##---------------------------------------------------------------------##
sub parseOutput {
my %parameters = @_;
croak $CLASS. "::parseWublastXOutput() missing searchOutput parameter!\n"
if ( !exists $parameters{'searchOutput'} );
my $WUFILE;
if ( ref( $parameters{'searchOutput'} ) !~ /GLOB|FileHandle/ ) {
print $CLASS
. "::parseWublastXOutput() Opening file "
. $parameters{'searchOutput'} . "\n"
if ( $DEBUG );
open $WUFILE, $parameters{'searchOutput'}
or die $CLASS
. "::parseWublastXOutput: Unable to open "
. "results file: $parameters{'searchOutput'} : $!";
}
else {
$WUFILE = $parameters{'searchOutput'};
}
my $cutoffP = -1;
if ( defined $parameters{'pValueCutoff'} ) {
$cutoffP = $parameters{'pValueCutoff'};
}
my @results = ();
my $queryID;
my $qryStart;
my $qrySeq;
my $qryEnd;
my $pValue;
my $score;
my $orientation;
my $sbjStart;
my $sbjEnd;
my $sbjSeq;
my $subjectID;
my $resultColl = SearchResultCollection->new();
my ( $matrixRef, $matrixAlphabet, $matrixFreqRef ) = _readMatrix();
my $lambda = _calculateLambda( $matrixRef, $matrixFreqRef );
#
while ( <$WUFILE> ) {
chomp;
if ( defined $qryStart
&& ( /^Query=/ || /^>/ || /^ Score =/ || /Strand HSPs/ ) )
{
if ( $cutoffP < 0 || $pValue <= $cutoffP ) {
# Complexity adjust the score
if ( defined $parameters{'scoreMode'}
&& $parameters{'scoreMode'} ==
SearchEngineI::complexityAdjustedScoreMode )
{
$score =
_complexityAdjust( $score, $qrySeq, $sbjSeq, $lambda,
$matrixAlphabet, $matrixRef, $matrixFreqRef );
}
if ( !defined $parameters{'scoreCutoff'}
|| $score >= $parameters{'scoreCutoff'} )
{
# Save the result
my $result = SearchResult->new(
queryName => $queryID,
queryStart => $qryStart,
queryEnd => $qryEnd,
#queryRemaining => ( $qryLength - $qryEnd ),
#queryString => $qrySeq,
#subjString => $sbjSeq,
orientation => $orientation,
subjName => $subjectID,
subjStart => $sbjStart,
subjEnd => $sbjEnd,
#subjRemaining => ( $sbjLength - $sbjEnd ),
#queryString => $qrySeq,
#pctDiverge => $percDiv,
#pctInsert => $percIns,
#pctDelete => $percDel,
pValue => $pValue,
score => $score
);
$resultColl->add( $result );
}
}
undef $qryStart;
undef $qryEnd;
$sbjStart = "";
$sbjEnd = "";
$qrySeq = "";
$sbjSeq = "";
}
if ( /^Query=\s+(\S+)/ ) {
$queryID = $1;
}
elsif ( /^>(\S+)/ ) {
$subjectID = $1;
}
elsif ( /^\s+(\w+) Strand HSPs:\s*$/ ) {
# TODO: Change this to +/-
if ( $1 eq "Minus" ) {
$orientation = "C";
}
else {
$orientation = "";
}
}
elsif ( /^ Score = (\d+) .+ (\S+)\s*$/ ) {
$score = $1;
$pValue = $2;
}
elsif ( /^Query:\s+(\d+)\s+(\S+)\s+(\d+)\s*$/ ) {
$qrySeq .= $2;
if ( $qryStart < 1 ) {
$qryStart = _min( $1, $3 );
$qryEnd = _max( $1, $3 );
}
else {
$qryStart = _min( _min( $1, $3 ), $qryStart );
$qryEnd = _max( _max( $1, $3 ), $qryEnd );
}
#$orientation = "C" if ( $1 > $3 );
}
elsif ( /Sbjct:\s+(\d+)\s+(\S+)\s+(\d+)/ ) {
$sbjSeq .= $2;
my $leftNum = $1;
my $rightNum = $3;
if ( $sbjStart < 1 ) {
$sbjStart = _min( $leftNum, $rightNum );
$sbjEnd = _max( $leftNum, $rightNum );
}
else {
$sbjStart = _min( _min( $leftNum, $rightNum ), $sbjStart );
$sbjEnd = _max( _max( $leftNum, $rightNum ), $sbjEnd );
}
}
}
if ( defined $qryStart && ( $cutoffP < 0 || $pValue <= $cutoffP ) ) {
# Complexity adjust the score
if ( defined $parameters{'scoreMode'}
&& $parameters{'scoreMode'} ==
SearchEngineI::complexityAdjustedScoreMode )
{
$score =
_complexityAdjust( $score, $qrySeq, $sbjSeq, $lambda, $matrixAlphabet,
$matrixRef, $matrixFreqRef );
}
if ( !defined $parameters{'scoreCutoff'}
|| $score >= $parameters{'scoreCutoff'} )
{
# Save the result
my $result = SearchResult->new(
queryName => $queryID,
queryStart => $qryStart,
queryEnd => $qryEnd,
#queryRemaining => ( $qryLength - $qryEnd ),
#queryString => $qrySeq,
#subjString => $sbjSeq,
orientation => $orientation,
subjName => $subjectID,
#subjStart => $sbjStart,
#subjEnd => $sbjEnd,
#subjRemaining => ( $sbjLength - $sbjEnd ),
#queryString => $qrySeq,
#pctDiverge => $percDiv,
#pctInsert => $percIns,
#pctDelete => $percDel,
pValue => $pValue,
score => $score
);
$resultColl->add( $result );
}
}
close $WUFILE;
return $resultColl;
}
##-------------------------------------------------------------------------##
## Private Methods
##-------------------------------------------------------------------------##
##-------------------------------------------------------------------------##
## Use: my _complexityAdjust( $swnScore, $qrySeq, $sbjSeq, $matLambda,
## $matAlphabet, $matScoresRef, $matFreqsRef );
##
## $swnScore : Smith-Waterman Raw Alignment Score
## $qrySeq : Query string from the alignment
## $sbjSeq : Subject string from the alignment
## $matLambda : Matrix Lambda parameter
## $matAlphabet : Matrix alphabet string (in column order)
## $matScoresRef: Score Matrix
## $matFreqsRef : Matrix alphabet freq vector
##
## Returns
## $adj_score : The complexity adjusted score according to
## to Phil Green's swat/cross_match program.
##-------------------------------------------------------------------------##
sub _complexityAdjust {
my ( $swnScore, $qrySeq, $sbjSeq, $matLambda, $matAlphabet, $matScoresRef,
$matFreqsRef )
= @_;
my $mCol = 0;
my $t_factor = 0;
my $t_sum = 0;
my $t_counts = 0;
my $n_letters = 0;
my $baseIndex = 0;
my $qBase = "";
my $sBase = "";
my $pos_score = 0;
my @matCounts = ();
my $adj_score = 0;
#
# Recalculates the raw score ( $pos_score ) based on the matrix we
# have been handed.
#
# Creates a vector of base counts from the query sequence. It
# ignores base instances when they are part of a deletion or
# are insertion characters "-".
#
for ( $baseIndex = 0 ; $baseIndex < length( $qrySeq ) ; $baseIndex++ ) {
$qBase = substr( $qrySeq, $baseIndex, 1 );
$sBase = substr( $sbjSeq, $baseIndex, 1 );
if ( $qBase ne "-" && $sBase ne "-" ) {
$pos_score +=
$$matScoresRef[ index( $matAlphabet, $qBase ) ]
[ index( $matAlphabet, $sBase ) ];
$matCounts[ index( $matAlphabet, $qBase ) ]++
if ( ( index $matAlphabet, $qBase ) >= 0 );
}
}
#print "Recalculated raw score = $pos_score\n";
#
#
#
for ( $mCol = 0 ; $mCol < length( $matAlphabet ) ; $mCol++ ) {
if ( defined $matCounts[ $mCol ] && $matCounts[ $mCol ] > 0 ) {
if ( $$matFreqsRef[ $mCol ] > 0 && log( $$matFreqsRef[ $mCol ] ) != 0 ) {
$t_factor += $matCounts[ $mCol ] * log( $matCounts[ $mCol ] );
$t_sum += $matCounts[ $mCol ] * log( $$matFreqsRef[ $mCol ] );
$t_counts += $matCounts[ $mCol ];
$n_letters++;
}
}
}
#
#
#
$t_factor -= $t_counts * log( $t_counts );
$t_sum -= $t_factor;
#
# Looks like Phil changed his mind here
#
#my $complexity_factor = 0.25;
#if ( $n_letters > ( 1 / $complexity_factor )) {
# $t_factor /= $t_counts * log(1 / $n_letters);
#}else {
# $t_factor /= $t_counts * log($complexity_factor);
#}
#
#$old_adj_score = $swnScore + ($t_factor * $pos_score) - $pos_score + .5;
#
#
#
$adj_score = sprintf( "%0.0d", $swnScore + $t_sum / $matLambda + .999 );
$adj_score = 0 if ( !( $adj_score =~ /\d+/ ) || $adj_score < 0 );
return ( $adj_score );
}
##-------------------------------------------------------------------------##
## Use: my _calculateLambda( $matScoresRef, $matFreqsRef );
##
## $matScoresRef: Score Matrix
## $matFreqsRef : Matrix alphabet freq vector
##
## Returns
## $lambda : The lambda parameter derived from the matrix
## and the matrix alphabet frequencies. This
## is derived from Phil Green's swat/cross_match
## programs.
##-------------------------------------------------------------------------##
sub _calculateLambda {
my ( $matScoresRef, $matFreqsRef ) = @_;
my $lambda_upper = 0;
my $lambda_lower = 0;
my $lambda = 0.5;
my $sum = 0;
do {
$sum = _getSum( $lambda, $matScoresRef, $matFreqsRef );
if ( $sum < 1.0 ) {
$lambda_lower = $lambda;
$lambda *= 2.0;
}
} while ( $sum < 1.0 );
$lambda_upper = $lambda;
while ( $lambda_upper - $lambda_lower > .00001 ) {
$lambda = ( $lambda_lower + $lambda_upper ) / 2.0;
$sum = _getSum( $lambda, $matScoresRef, $matFreqsRef );
if ( $sum >= 1.0 ) {