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WUBlastSearchEngine.pm
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WUBlastSearchEngine.pm
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#!/usr/bin/perl -w
##---------------------------------------------------------------------------##
## File:
## @(#) WUBlastSearchEngine.pm
## Author:
## Robert M. Hubley rhubley@systemsbiology.org
## Description:
## An implementation of SearchEngineI for the
## the WU-Blast/AB-Blast 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(
# 'WUBlastSearchEngine' );
#
###############################################################################
# ChangeLog
#
# $Log$
#
###############################################################################
# To Do:
#
#
=head1 NAME
WUBlastSearchEngine
=head1 SYNOPSIS
use WUBlastSearchEngine
Usage:
use SearchEngineI;
use WUBlastSearchEngine;
use SearchResultCollection;
my $wuEngine = WUBlastSearchEngine->new(
pathToEngine=>"/usr/local/wublast/blastp" );
$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 WUBlast sequence search engine.
=head1 INSTANCE METHODS
=cut
package WUBlastSearchEngine;
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 ] );
#
# Version
#
my $VERSION = 0.1;
my $CLASS = "WUBlastSearchEngine";
##-------------------------------------------------------------------------##
## 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'} );
# TODO: Figure out a better design
$this->setUseDustSeg( 1 );
# Allow import of values
if ( %nameValuePairs ) {
while ( my ( $name, $value ) = each( %nameValuePairs ) ) {
my $method = "set" . _ucFirst( $name );
unless ( $this->can( $method ) ) {
croak( "$CLASS::set: Instance variable $name doesn't exist." . "" );
}
$this->$method( $value );
}
}
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 UseDustSeg()
Use: my $value = getUseDustSeg( );
Use: my $oldValue = setUseDustSeg( $value );
Turn on / off the Dust/Seg screening of words.
=cut
##-------------------------------------------------------------------------##
sub getUseDustSeg {
my $this = shift;
return $this->{'useDustSeg'};
}
sub setUseDustSeg {
my $this = shift;
my $value = shift;
my $oldValue = $this->{'useDustSeg'};
$this->{'useDustSeg'} = $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`;
# BLASTN 3.0-SE [2009-05-25] [linux26-x64-I32LPF64 2009-05-25T22:58:29]
if ( $result =~ /^(BLAST[PN]) (\S+ \[.*\])/ ) {
$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 getParameters()
Use: my $wuBlastParamString = getParameters( );
Convert object parameters into WUBlast command line parameters.
=cut
##-------------------------------------------------------------------------##
sub getParameters {
my $this = shift;
# 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() ) ) {
# The -span1 and -span2 parameters ( from the wublast
# manual for -span1 ):
# "This option relaxes the criteria for judging whether an HSP
# spans another, prior to discarding one of them if spanning is
# detected. With this option, it is merely a matter of either the query
# seg-ment or the database segment (or both) spans the corresponding
# segment(s) in the other HSP, whereas the -span2 option requires
# that both segments be spanned. The -span1 option may be useful in
# suppressing reports of HSPs when the query or a database sequence
# contains internal repeats."
# MaskerAid used -span1 for dealing with simple repeats. The
# only way to catch that is to check for the name of the lib.
# This is a hack and I am not very happy about it.
# Decide when to use the span1 parameter:
if ( $value =~ /simple.lib/ || $value =~ /at.lib/ ) {
$spanParameter = " -span1";
}
# Make sure we have the compressed form of the database handy
if ( -f "$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";
}
if ( ( $value = $this->getQuery() ) ) {
if ( -f $value ) {
$parameters .= " $value";
# TODO: Figure out a better design
if ( $value =~ /simple.lib/ || $value =~ /at.lib/ ) {
$spanParameter = " -span1";
}
}
else {
croak $CLASS. "::search: Error...query ($value) does not exist!\n";
}
}
else {
croak $CLASS. "::search: Error query undefined!\n";
}
# Constant parameters
if ( $this->{'engineName'} eq "BLASTP" ) {
$parameters .= " -warnings -T=1000000 -hspmax=2000000000 -gi ";
$parameters .= " V=0 B=100000000";
}
elsif ( $this->{'engineName'} eq "BLASTN" ) {
$parameters .= " -warnings -kap -gi";
if ( $this->{'useDustSeg'} >= 1 ) {
$parameters .= " wordmask=dust wordmask=seg";
}
$parameters .= " maskextra=10 -hspmax=0 V=0 B=100000000";
}
else {
croak $CLASS
. "::search: Could not determine default parameters "
. " for engineName ( "
. $this->{'engineName'} . " )!\n";
}
$parameters .= $spanParameter;
if ( defined( $value = $this->getGapInit() )
&& $value =~ /\d+/ )
{
$parameters .= " Q=" . abs( $value );
}
else {
$parameters .= " Q=12";
}
if ( defined( $value = $this->getInsGapExt() )
&& $value =~ /\d+/ )
{
$parameters .= " R=" . abs( $value );
}
else {
$parameters .= " R=2";
}
if ( defined( $value = $this->getMinMatch() )
&& $value =~ /\d+/ )
{
$parameters .= " W=$value";
}
else {
$parameters .= " W=14";
}
# 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 );
}
else {
$parameters .= " S=30";
$parameters .= " gapS2=30";
$parameters .= " S2=15";
$parameters .= " X=30";
$parameters .= " gapX=60";
}
if ( defined( $value = $this->getBandwidth() )
&& $value =~ /\d+/ )
{
$parameters .= " gapW=" . ( ( $value * 3 ) + 1 );
}
if ( defined( $value = $this->getCores() ) ) {
$parameters .= " -cpus=$value ";
}
else {
$parameters .= " -cpus=4 ";
}
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;
$parameters .= " -matrix=$matrix";
}
else {
croak $CLASS. "::search: Error...matrix ($value) does not exist!\n";
}
}
my $runParameters;
if ( defined $this->{'overrideParameters'}
&& $this->{'overrideParameters'} ne "" )
{
$runParameters = $this->{'overrideParameters'};
}
else {
$runParameters = $parameters . " ";
}
if ( defined $this->{'additionalParameters'}
&& $this->{'additionalParameters'} ne "" )
{
$runParameters .= " " . $this->{'additionalParameters'};
}
return ( "$engine $runParameters" );
}
##-------------------------------------------------------------------------##
=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 );
}
}
# Form the command line
my $cmdLine = $this->getParameters();
my $matrixName;
if ( defined( my $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 );
$matrixName = 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};
$ENV{ABBLASTMAT} = $ENV{BLASTMAT};
}
else {
croak $CLASS. "::search: Error...matrix ($value) does not exist!\n";
}
}
my $outputDirName;
if ( defined $this->getTempDir() && -d $this->getTempDir() ) {
$outputDirName = $this->getTempDir();
}
else {
$outputDirName = dirname( $this->getQuery() );
}
# Invoke engine and handle errors
my $POUTPUT = new FileHandle;
my $errFile;
my $currentTime;
do {
$currentTime = time();
$errFile = $outputDirName . "/wuResults-$currentTime-$$.err";
} while ( -f $errFile );
my $pid;
print $CLASS
. "::search() Invoking search engine as: $cmdLine "
. " 2>$errFile |\n"
if ( $this->getDEBUG() );
my %parseParams = ();
$parseParams{'debug'} = $this->getDEBUG() if ( $this->getDEBUG() );
$parseParams{'excludeAlignments'} = 1
if ( !$this->getGenerateAlignments()
&& $this->getScoreMode() != SearchEngineI::complexityAdjustedScoreMode );
$parseParams{'matrixName'} = $matrixName;
# Create SearchResultCollection object from
# the engine results.
my $searchResultsCollection;
$pid = open( $POUTPUT, "$cmdLine 2>$errFile |" );
## Create a debug file
my $outFile = $outputDirName . "/wuResults-$currentTime-$$.out";
open OUT, ">$outFile";
while ( <$POUTPUT> ) {
print OUT $_;
}
close OUT;
close $POUTPUT;
$parseParams{'searchOutput'} = $outFile;
$searchResultsCollection = parseOutput( %parseParams );
my $resultCode = ( $? >> 8 );
print "WUBlast returned a the following result code >$resultCode<\n"
if ( $this->getDEBUG() );
# 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 );
}
#
# Postprocess the results
#
if ( defined $searchResultsCollection
&& $searchResultsCollection->size() > 0 )
{
#
# Apply minscore filter on raw scores or
# complexity adjusted scores depending on settings.
#
my $complexityAdjust = 0;
my $matrixObj;
my $gapOpen;
my $gapInsExtn;
my $gapDelExtn;
my $minScore;
$minScore = $this->getMinScore() if ( $this->getMinScore() );
if ( $this->getScoreMode() == SearchEngineI::complexityAdjustedScoreMode ) {
$complexityAdjust = 1;
$matrixObj = Matrix->new( fileName => $this->getMatrix() );
$matrixObj->transposeMatrix();
$gapOpen = $this->getGapInit();
$gapInsExtn = $this->getInsGapExt();
$gapDelExtn = $this->getDelGapExt();
if ( !$matrixObj ) {
croak "Cannot apply complexity adjustment without"
. " matrix and gap scores!\n";
}
}
if ( $minScore || $complexityAdjust ) {
print $CLASS
. "::search: "
. $searchResultsCollection->size()
. " hits before complexityAdjust/minScore filtering\n"
if ( $this->getDEBUG() );
for ( my $i = $searchResultsCollection->size() - 1 ; $i >= 0 ; $i-- ) {
my $result = $searchResultsCollection->get( $i );
if ( $complexityAdjust ) {
my ( $newScore, $kimura ) = $result->rescoreAlignment(
scoreMatrix => $matrixObj,
gapOpenPenalty => $gapOpen,
insGapExtensionPenalty => $gapInsExtn,
delGapExtensionPenalty => $gapDelExtn,
divCpGMod => 1,
complexityAdjust => 1
);
if ( $minScore && $newScore < $minScore ) {
$searchResultsCollection->remove( $i );
next;
}
$result->setScore( $newScore );
$result->setPctKimuraDiverge( sprintf( "%4.2f", $kimura ) );
}
else {
if ( $minScore && $result->getScore() < $minScore ) {
$searchResultsCollection->remove( $i );
next;
}
# Do not complexity adjust...but we should record the
# divergence. Use a much faster routine to calculate
# only divergence
my ( $div, $transi, $transv, $wellCharBases, $numCpGs ) =
$result->calcKimuraDivergence( divCpGMod => 1 );
$result->setPctKimuraDiverge( sprintf( "%4.2f", $div ) );
}
# Only keep alignment data if requested
#if ( !$this->getGenerateAlignments() )
#{
# $result->setQueryString( "" );
# $result->setSubjString( "" );
#}
}
print $CLASS
. "::search: "
. $searchResultsCollection->size()
. " hits after complexityAdjust/minScore filtering\n"
if ( $this->getDEBUG() );
}
#
# Mask level filtering
#
my $maskLevel;
my $strand;
if ( $searchResultsCollection->size() > 0
&& defined( $maskLevel = $this->getMaskLevel() )
&& $maskLevel > 0 )
{
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 ( $this->getDEBUG() );
}
# The final result collection should be sorted by
# queryname and secondarily by query start position.
$searchResultsCollection->sort(
sub ($$) {
$_[ 0 ]->getQueryName cmp $_[ 1 ]->getQueryName()
|| $_[ 0 ]->getQueryStart() <=> $_[ 1 ]->getQueryStart();
}
);
}
unless ( $this->getDEBUG() || $resultCode ) {
unlink $errFile;
unlink $outFile;
return ( $resultCode, $searchResultsCollection );
}
else {
return ( $resultCode, $searchResultsCollection, $outFile, $errFile );
}
}
##-------------------------------------------------------------------------##
=head1 Class Methods
=cut
##-------------------------------------------------------------------------##
##-------------------------------------------------------------------------##
=head2 parseOutput()
Use: my $SearchResultCollection = WUBLASTSearchEngine::parseOutput(
searchOutput => $filename|$FH,
[matrixName => $matrixName],
[excludeAlignments => 1] );
Parse the result of a search and return a SearchResultCollection.
NOTE: Providing a scoreMatrix parameter turns on complexity
score adjustment.
=cut
##-------------------------------------------------------------------------##
sub parseOutput {
my %nameValueParams = @_;
croak $CLASS. "::parseOutput() missing searchOutput parameter!\n"
if ( !exists $nameValueParams{'searchOutput'} );
my $WUFILE;
if ( ref( $nameValueParams{'searchOutput'} ) !~ /GLOB|FileHandle/ ) {
print $CLASS
. "::parseOutput() Opening file "
. $nameValueParams{'searchOutput'} . "\n"
if ( $nameValueParams{'debug'} );
open $WUFILE, $nameValueParams{'searchOutput'}
or die $CLASS
. "::parseOutput: Unable to open "
. "results file: $nameValueParams{'searchOutput'} : $!";
}
else {
$WUFILE = $nameValueParams{'searchOutput'};
}
my $callbackFunc = undef;
if ( defined $nameValueParams{'callback'}
&& ref( $nameValueParams{'callback'} ) == /CODE/ )
{
## TODO: Add warning if it's not code
$callbackFunc = $nameValueParams{'callback'};
}
my $inAlignState = 0;
my $sbjID = "";
my $qryID = "";
my $absIndex = 0;
my $score = 0;
my $adjScore = 0;
my $sbjSeq = "";
my $qrySeq = "";
my $sbjOrient = "";
my $qryOrient = ""; # TODO: Check to see if this ever happens
my $sbjStart = 0;
my $sbjEnd = 0;
my $qryStart = 0;
my $qryEnd = 0;
my $qryLength = 0;
my $sbjLength = 0;
my $matrix = "";
my $evalue = 0;
my $resultColl = SearchResultCollection->new();
while ( <$WUFILE> ) {
#
# Conditions for the end of a hit record:
# o Must have seen a score
# o Must be in the alignment state (ie. have seen Query: and
# Subj: recently)
# o Must see something which isn't either "Query:" "Subj:" or " "
# or must see the end of the file
#
if ( $inAlignState ) {
if ( !/^(Query:|Sbjct:|\s{8}|\n|\r)/ || eof ) {
#
# Reorient if this is a reverse strand
# hit.
#
my $orientation = "";
if ( $qryOrient eq "C" ) {
# Fix the sequence orientation so that it
# matches the SearchResult.pm convention of
# the query being in the forward direction.
$qrySeq = reverse $qrySeq;
$qrySeq =~ tr/ACGTYRMKHBVD/TGCARYKMDVBH/; # complement
$sbjSeq = reverse $sbjSeq;
$sbjSeq =~ tr/ACGTYRMKHBVD/TGCARYKMDVBH/; # complement
$orientation = "C";
}
elsif ( $sbjOrient eq "C" ) {
# Fix the subject coordinates since they
# are based on a pre-reversed sequence.
my $tmpEnd = $sbjEnd;
$sbjEnd = $sbjLength - $sbjStart + 1;
$sbjStart = $sbjLength - $tmpEnd + 1;
$orientation = "C";
}
#
# Calculate percent divergence
# percent insertions
# percent deletions
#
my %baseFreq = ();
my $mismatch = 0;
for ( my $i = 0 ; $i < length( $qrySeq ) ; $i++ ) {
my $qryBase = substr( $qrySeq, $i, 1 );
my $sbjBase = substr( $sbjSeq, $i, 1 );
next if ( $qryBase =~ /-|x/i || $sbjBase =~ /-|x/i );
$baseFreq{$qryBase}++;
$mismatch++ if ( $qryBase ne $sbjBase );
}
my $percDiv =
sprintf( "%4.2f", $mismatch * 100 / ( $qryEnd + 1 - $qryStart ) );
my $qgap = $qrySeq =~ tr/-/-/;
my $sgap = $sbjSeq =~ tr/-/-/;
my $percIns =
sprintf( "%4.2f", $sgap * 100 / ( ( $sbjEnd + 1 ) - $sbjStart ) );
my $percDel =
sprintf( "%4.2f", $qgap * 100 / ( ( $qryEnd + 1 ) - $qryStart ) );
if ( defined( $nameValueParams{'excludeAlignments'} ) ) {
$qrySeq = "";
$sbjSeq = "";
}
$matrix = $nameValueParams{'matrixName'}
if ( defined( $nameValueParams{'matrixName'} ) );
my $result = SearchResult->new(
queryName => $qryID,
queryStart => $qryStart,
queryEnd => $qryEnd,
queryRemaining => ( $qryLength - $qryEnd ),
queryString => $qrySeq,
subjString => $sbjSeq,
orientation => $orientation,
subjName => $sbjID,
subjStart => $sbjStart,
subjEnd => $sbjEnd,
subjRemaining => ( $sbjLength - $sbjEnd ),
pctDiverge => $percDiv,
pctInsert => $percIns,
pctDelete => $percDel,
matrixName => $matrix,
score => $score,
EValue => $evalue
);
if ( defined $callbackFunc ) {
$callbackFunc->( $result );
}
else {
$resultColl->add( $result );
}
$score = "";
$sbjSeq = "";
$qrySeq = "";
$qryOrient = "";
$sbjStart = 0;
$sbjEnd = 0;
$qryStart = 0;
$qryEnd = 0;
$inAlignState = 0;
$evalue = 0;
}
}
#
# Query alignment
#
if ( /Query:\s+(\d+)\s+(\S+)\s+(\d+)/ ) {
$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 );
}
$qryOrient = "C" if ( $1 > $3 );
$inAlignState = 1;
}
#
# Subject alignment
#
if ( /Sbjct:\s+(\d+)\s+(\S+)\s+(\d+)/ ) {
$sbjSeq .= $2;
my $leftNum = $1;
my $rightNum = $3;
if ( $leftNum > $rightNum ) {
if ( ( $leftNum - $rightNum ) == 1 ) {
# There is currently a bug in blast. It occasionally
# mis-indexes the alignment data so that the last
# line contains an index which is descending.
$leftNum = $3;
$rightNum = $1;
}
else {
croak $CLASS
. "::parseOutput: Strange blast alignment format. "
. "The subject sequence should not contain descending "
. "indexes: ( $_ )!\n";
}
}
if ( $sbjStart < 1 ) {
$sbjStart = _min( $leftNum, $rightNum );
$sbjEnd = _max( $leftNum, $rightNum );
}
else {
$sbjStart = _min( _min( $leftNum, $rightNum ), $sbjStart );
$sbjEnd = _max( _max( $leftNum, $rightNum ), $sbjEnd );