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Refiner
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#!/u1/local/bin/perl
##---------------------------------------------------------------------------##
## File:
## @(#) Refiner
## Author:
## Arian Smit <[email protected]>
## Robert Hubley <[email protected]>
## Description:
## Given a set of instances of a particular interspersed
## repeat develop and refine a consensus model for
## them.
##
#******************************************************************************
#* Copyright (C) Institute for Systems Biology 2008 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.
#*
###############################################################################
# ChangeLog:
#
# $Log: Refiner,v $
# Revision 1.37 2017/04/05 00:03:31 rhubley
# Cleanup before a distribution
#
#
###############################################################################
#
# To Do:
#
#
#
# Module Dependence
#
use strict;
use FindBin;
use lib $FindBin::RealBin;
use Getopt::Long;
use POSIX qw(:sys_wait_h);
use File::Copy;
use File::Spec;
use File::Path;
use File::Basename;
use Cwd;
use Data::Dumper;
# RepeatModeler Libraries
use RepModelConfig;
use lib $RepModelConfig::REPEATMASKER_DIR;
use MultAln;
use NeedlemanWunschGotohAlgorithm;
# RepeatMasker Libraries
use SearchResult;
use SearchResultCollection;
use WUBlastSearchEngine;
use NCBIBlastSearchEngine;
use SequenceSimilarityMatrix;
use SeqDBI;
use SimpleBatcher;
use FastaDB;
#
# Class Globals & Constants
#
my $CLASS = "Refiner";
my $DEBUG = 0;
$DEBUG = 1 if ( $RepModelConfig::DEBUGALL == 1 );
$| = 1; # Turn autoflush on
#
# Version
# -- NOTE: This is filled in by configure
my $version = "#VERSION#";
$version = "DEV" if ( $version =~ /\#VERSION\#/ );
if ( $ARGV[ 0 ] && $ARGV[ 0 ] eq '-v' )
{
print "Refiner version $version\n";
exit;
}
#
# Option processing
# e.g.
# -t: Single letter binary option
# -t=s: String parameters
# -t=i: Number paramters
#
my @opts = qw( help noTmp debug engine=s giToID=s );
#
# Get the supplied command line options, and set flags
#
my %options = ();
unless ( &GetOptions( \%options, @opts ) )
{
exec "pod2text $0";
exit( 1 );
}
# Print the internal POD documentation if something is missing
if ( $#ARGV == -1 || $options{'help'} )
{
print "No query sequence file indicated\n\n";
# This is a nifty trick so we don't have to have
# a duplicate "USAGE()" subroutine. Instead we
# just recycle our POD docs. See PERL POD for more
# details.
exec "pod2text $0";
die;
}
$DEBUG = 1 if ( $options{'debug'} );
#
# If used as part of the RepeatModeler system
# read in the seq IDs from the original database
# so we can place them in the stockholm file.
#
my %genomeDBToSeqID = ();
if ( $options{'giToID'} )
{
open IN, "<$options{'giToID'}"
or die "Could not open $options{'giToID'} file for reading!\n";
while ( <IN> )
{
if ( /^(\S+)\s+(\d+)/ )
{
$genomeDBToSeqID{"gi|$2"} = $1;
}
}
close IN;
}
#
# Setup the search engines
#
my $srchEngAllVsAll;
my $srchEngOneVsAll;
my $engine = $RepModelConfig::DEFAULT_SEARCH_ENGINE;
$engine = $options{'engine'} if ( $options{'engine'} );
if ( $engine )
{
if ( $engine =~ /wublast|abblast/i )
{
$engine = "abblast";
$srchEngAllVsAll =
WUBlastSearchEngine->new(
pathToEngine => $RepModelConfig::WUBLASTN_PRGM );
$srchEngOneVsAll =
WUBlastSearchEngine->new(
pathToEngine => $RepModelConfig::WUBLASTP_PRGM );
if ( not defined $srchEngAllVsAll )
{
die
"Refiner Failed: Cannot execute $RepModelConfig::WUBLASTN_PRGM please make "
. "sure you have setup RepeatModeler to use AB/WUBlast "
. "by running the configure script.\n";
}
} elsif ( $engine =~ /ncbi/i )
{
$engine = "ncbi";
$srchEngAllVsAll =
NCBIBlastSearchEngine->new(
pathToEngine => $RepModelConfig::RMBLASTN_PRGM );
$srchEngOneVsAll =
NCBIBlastSearchEngine->new(
pathToEngine => $RepModelConfig::RMBLASTN_PRGM );
if ( not defined $srchEngAllVsAll )
{
die
"Refiner Failed: Cannot execute $RepModelConfig::RMBLASTN_PRGM please make "
. "sure you have setup RepeatModeler to use NCBI (RMBlast) by "
. "running the configure script.\n";
}
} else
{
print "I don't recognize the search engine type: $engine\n";
exec "pod2text $0";
die;
}
}
#
# Parse filenames
#
foreach my $file ( @ARGV )
{
if ( $file =~ /\s/ )
{
die "RepeatModeler can not handle filenames with spaces "
. "like the file \"$file\"\n";
} elsif ( $file =~ /([\`\!\$\^\&\*\(\)\{\}\[\]\|\\\;\"\'\<\>\?])/ )
{
die "RepeatModeler can not handle filenames with the special "
. "character \"$1\" as in the file \"$file\"\n";
}
}
my @tmpDirPath = ( cwd(), ( File::Spec->splitpath( $ARGV[ 0 ] ) )[ 1 ] );
print "TempDirPath = " . join( ", ", @tmpDirPath ) . "\n" if ( $DEBUG );
my $tmpDir;
#
# Main loop
#
my @TimeBefore = ();
elapsedTime( 0 );
foreach my $file ( @ARGV )
{
unless ( -r $file )
{
print "cannot read file $file\n";
next;
}
print "\nanalyzing file $file\n" if ( $#ARGV >= 0 && $DEBUG );
$tmpDir = dirname( $file );
unless ( $options{'noTmp'} )
{
$tmpDir = createTempDir( \@tmpDirPath );
}
print "Tmpdir = $tmpDir\n" if ( $DEBUG );
my ( $cons, $maSize, $avgKDiv ) = &buildConsensus(
$RepModelConfig::REPEATMODELER_MATRICES_DIR,
$RepModelConfig::XDFORMAT_PRGM,
$srchEngAllVsAll,
$srchEngOneVsAll,
$file,
$tmpDir
);
$cons =~ s/-//g;
open OUTC, ">$file.refiner_cons";
# Save the consensus to the consensi file.
print OUTC ">family ( Final Multiple Alignment Size = " . $maSize
. " , Avg Kimura = $avgKDiv )\n";
print OUTC "$cons\n";
close OUTC;
}
##########################################################################
##########################################################################
##########################################################################
##########################################################################
sub buildConsensus
{
my $matrixDir = shift;
my $xdformatPrgm = shift;
my $srchEngAllVsAll = shift();
my $srchEngOneVsAll = shift();
my $pathToFastaFile = shift();
my $wrkDir = shift();
# Break down fastaFile path to directory/file
# components
my $consName = basename( $pathToFastaFile );
# TODO: This is a hack!
$consName =~ s/\.fa//g;
my $cons = "";
my $db;
my @multiSeqs = ();
my %uniqSeqIDs = ();
my $finalMultiAlignmentSize = 0;
my $avgKDiv = 0;
my $round1ConsLen = 0;
my $round1NumUnAlignSeqs = 0;
if ( $DEBUG )
{
print "========================="
. $consName
. "=========================\n";
print " -------------------ROUND 1 ------------------ \n";
}
## Build database of input file
if ( $engine eq "abblast" )
{
# Build wublast databases for fasta file.
system(
"$xdformatPrgm -n $pathToFastaFile >> " . "$wrkDir/setdb.log 2>&1" );
$srchEngAllVsAll->setMatrix( "$matrixDir/wublast/nt/comparison.matrix" );
$srchEngOneVsAll->setMatrix( "$matrixDir/wublast/aa/comparison.matrix" );
} else
{
# MAKEBLASTDB the database
#. "-parse_seqids -dbtype nucl -in $pathToFastaFile >> "
system( "$RepModelConfig::NCBIBLASTDB_PRGM -out $pathToFastaFile "
. "-dbtype nucl -in $pathToFastaFile >> "
. "$wrkDir/makeblastdb.log 2>&1" );
$srchEngAllVsAll->setMatrix( "$matrixDir/ncbi/nt/comparison.matrix" );
$srchEngOneVsAll->setMatrix( "$matrixDir/ncbi/nt/comparison.matrix" );
}
## Setup the general search parameters
$srchEngAllVsAll->setMinScore( 150 );
$srchEngAllVsAll->setGenerateAlignments( 1 );
$srchEngAllVsAll->setGapInit( -25 );
$srchEngAllVsAll->setInsGapExt( -5 );
$srchEngAllVsAll->setDelGapExt( -5 );
$srchEngAllVsAll->setMinMatch( 7 );
$srchEngAllVsAll->setTempDir( dirname( $pathToFastaFile ) );
$srchEngAllVsAll->setScoreMode( SearchEngineI::complexityAdjustedScoreMode );
$srchEngOneVsAll->setMinScore( 150 );
$srchEngOneVsAll->setGenerateAlignments( 1 );
$srchEngOneVsAll->setGapInit( -25 );
$srchEngOneVsAll->setInsGapExt( -5 );
$srchEngOneVsAll->setDelGapExt( -5 );
$srchEngOneVsAll->setMinMatch( 7 );
$srchEngOneVsAll->setTempDir( dirname( $pathToFastaFile ) );
$srchEngOneVsAll->setScoreMode( SearchEngineI::complexityAdjustedScoreMode );
$srchEngOneVsAll->setMaskLevel( 80 );
# Search family file against itself.
$srchEngAllVsAll->setQuery( $pathToFastaFile );
$srchEngAllVsAll->setSubject( $pathToFastaFile );
print $CLASS
. "::buildConsensus(): Running All-vs-All "
. "on $pathToFastaFile \n"
if ( $DEBUG );
my $round = "1";
my ( $runStat, $familyCollection ) = $srchEngAllVsAll->search();
## Cleanup after run
if ( $engine eq "abblast" )
{
# Remove wublast databases
system( "rm $pathToFastaFile.xn*" ) unless ( $DEBUG );
} else
{
# Remove ncbi databases
system( "rm $pathToFastaFile.nin "
. "$pathToFastaFile.nhr $pathToFastaFile.nsq " )
unless ( $DEBUG );
}
print $CLASS
. "::buildConsensus(): Returned "
. $familyCollection->size()
. " hits\n"
if ( $DEBUG );
my $malign;
my $unalignedFastaSeqs = "";
if ( $runStat )
{
print STDERR "\nERROR from search engine (", $? >> 8, ") \n";
} else
{
## Find highest scoring element
my $MOUT;
open $MOUT, ">$wrkDir/$consName-cons.html";
my $refID =
&findHighestScoringAlignmentSet(
searchCollection => $familyCollection );
if ( $familyCollection->size() > 0 )
{
$db = FastaDB->new( fileName => $pathToFastaFile,
openMode => SeqDBI::ReadOnly );
# Grab the reference sequence
my $refSeq = $db->getSequence( $refID );
# Develop a pseudo mutiple alignment based on the
# remaining common sequence alignments.
$malign = MultAln->new(
referenceSeq => $refSeq,
searchCollection => $familyCollection,
searchCollectionReference => MultAln::Query,
flankingSequenceDatabase => $db,
maxFlankingSequenceLen => -1
);
$cons = $malign->consensus( "$matrixDir/linupmatrix" );
my (
$leftMostSequence, $leftMostSequenceID,
$rightMostSequence, $rightMostSequenceID
)
= &getLongestFlankingExtension( multAln => $malign );
writeHTMLMultAlign(
multAln => $malign,
destination => $MOUT,
leftFlankingID => $leftMostSequenceID,
rightFlankingID => $rightMostSequenceID
);
$malign->serializeOUT( "$wrkDir/$consName-cons.malign" );
undef $malign;
# Print unalignable sequences
my %seqNames = ();
my $qryID = $familyCollection->get( 0 )->getQueryName();
$seqNames{$qryID} = 1;
for ( my $j = 0 ; $j < $familyCollection->size() ; $j++ )
{
my $sbjID = $familyCollection->get( $j )->getSubjName();
$seqNames{$sbjID} = 1;
}
my $unAlignSeqs = "";
my $numUnAlignSeqs = 0;
foreach my $seqID ( $db->getIDs() )
{
unless ( exists $seqNames{$seqID} )
{
$unAlignSeqs .=
"Unaligned ( $seqID ): " . $db->getSequence( $seqID ) . "\n";
$numUnAlignSeqs++;
}
}
if ( $numUnAlignSeqs > 0 )
{
print $MOUT "$numUnAlignSeqs sequences could not be aligned to "
. "this particular reference sequence:\n";
print $MOUT "<PRE>\n$unAlignSeqs\n</PRE>\n";
}
print $CLASS
. "::buildConsensus(): "
. $familyCollection->size()
. " elements left after initial multiple alignment\n"
if ( $DEBUG );
## Build Consensus
$cons =~ s/-//g;
$round1ConsLen = length( $cons );
$round1NumUnAlignSeqs = $numUnAlignSeqs;
if ( $DEBUG )
{
print " - Unaligned sequences = $numUnAlignSeqs\n";
print " - Consensus Length = " . length( $cons ) . "\n";
}
##########################################
######### Consensus refinement ###########
##########################################
my $prevCons = "";
my $newConsBlocks;
my $finalRound = 0;
do
{
print $MOUT "\n<br>\n<br><hr>\n<br>\n<br>";
$round++;
if ( $DEBUG )
{
print " -------------------ROUND $round ------------------ \n";
}
$prevCons = $cons;
# Save the consensus to a fasta file
open CONF, ">$wrkDir/$consName-cons-$round.fa";
print CONF ">$consName ( "
. $familyCollection->size()
. " hsps from initial "
. "mulitiple alignment)\n";
my $consFa = $cons;
$consFa =~ s/-//g;
print CONF "$consFa\n";
close CONF;
$leftMostSequence = "";
$rightMostSequence = "";
if ( $engine eq "abblast" )
{
system( "$xdformatPrgm -p $wrkDir/$consName-cons-$round.fa >> "
. "$wrkDir/setdb.log 2>&1" );
} else
{
# MAKEBLASTDB the database
#. "-parse_seqids -dbtype nucl -in "
system( "$RepModelConfig::NCBIBLASTDB_PRGM -out "
. "$wrkDir/$consName-cons-$round.fa "
. "-dbtype nucl -in "
. "$wrkDir/$consName-cons-$round.fa >> "
. "$wrkDir/makeblastdb.log 2>&1" );
}
# Setup the search parameters
$srchEngOneVsAll->setSubject( "$wrkDir/$consName-cons-$round.fa" );
$srchEngOneVsAll->setQuery( $pathToFastaFile );
print $CLASS
. "::buildConsensus(): Cons-vs-All WUBlastP "
. "$consName\n"
if ( $DEBUG );
print "Params: " . $srchEngOneVsAll->getParameters() . "\n"
if ( $DEBUG );
( $runStat, $familyCollection ) = $srchEngOneVsAll->search();
if ( $engine eq "abblast" )
{
# Remove the wublast databases
system( "rm $wrkDir/$consName-cons-$round.fa.xp*" ) unless ( $DEBUG );
} else
{
# Remove the ncbi databases
system( "rm $wrkDir/$consName-cons-$round.fa.n*" ) unless ( $DEBUG );
}
print $CLASS
. "::buildConsensus(): AB/RM Blast returned "
. $familyCollection->size()
. " hits\n"
if ( $DEBUG );
if ( $runStat )
{
print STDERR "\nERROR from search engine (", $? >> 8, ") \n";
} else
{
# Create multiple alignment of results
$malign = MultAln->new(
referenceSeq => $consFa,
searchCollection => $familyCollection,
searchCollectionReference => MultAln::Subject,
flankingSequenceDatabase => $db,
maxFlankingSequenceLen => -1
);
# Build consensus
$cons = $malign->consensus( "$matrixDir/linupmatrix" );
my $sumDiv = $malign->kimuraDivergence( $cons );
$avgKDiv = 0;
if ( $malign->getNumAlignedSeqs() > 0 )
{
$avgKDiv = $sumDiv / $malign->getNumAlignedSeqs();
}
$malign->serializeOUT( "$wrkDir/$consName-malign-$round.ser" )
if ( $DEBUG );
# Determine if we are at the end of our loop
if ( $finalRound == 0 && ( $prevCons eq $cons || $round == 10 ) )
{
if ( $DEBUG )
{
print " - Consensus stable...resolving low quality blocks..\n";
}
$newConsBlocks = resolveLowQualityBlocks( multAln => $malign );
# Patch up the cons
for ( my $j = 0 ; $j <= $#{$newConsBlocks} ; $j++ )
{
my $colWidth =
$newConsBlocks->[ $j ]->{'end'} -
$newConsBlocks->[ $j ]->{'start'} + 1;
my $colSeq = $newConsBlocks->[ $j ]->{'cons'};
my $seq = $colSeq . "-" x ( $colWidth - length( $colSeq ) );
substr( $cons, $newConsBlocks->[ $j ]->{'start'}, length( $seq ) )
= $seq;
}
writeHTMLMultAlign(
multAln => $malign,
destination => $MOUT,
leftFlankingID => $leftMostSequenceID,
rightFlankingID => $rightMostSequenceID,
printHistogram => 1,
newConsBlocks => $newConsBlocks,
finalConsensus => $cons
);
$finalRound++;
} else
{
$finalRound++ if ( $finalRound == 1 );
if ( $finalRound == 2 )
{
# TODO: Put this back when we work on this again
#writeHTMLMultAlign(
# multAln => $malign,
# destination => $MOUT,
# leftFlankingID => $leftMostSequenceID,
# rightFlankingID => $rightMostSequenceID,
# printDupDelCols => 1
#);
writeHTMLMultAlign(
multAln => $malign,
destination => $MOUT,
leftFlankingID => $leftMostSequenceID,
rightFlankingID => $rightMostSequenceID,
);
} else
{
writeHTMLMultAlign(
multAln => $malign,
destination => $MOUT,
leftFlankingID => $leftMostSequenceID,
rightFlankingID => $rightMostSequenceID
);
}
#$malign->_getEndStartPairs() if ( $finalRound == 2 );
}
# Determine which sequences were not aligned.
my %seqNames = ();
my $sbjID = $familyCollection->get( 0 )->getSubjName();
$seqNames{$sbjID} = 1;
for ( my $j = 0 ; $j < $familyCollection->size() ; $j++ )
{
# Testing
#print "OUT: "
# . $familyCollection->get( $j )
# ->toStringFormatted( SearchResult::AlignWithQuerySeq ) . "\n";
my $qryID = $familyCollection->get( $j )->getQueryName();
$seqNames{$qryID} = 1;
}
$unAlignSeqs = "";
$unalignedFastaSeqs = "";
$numUnAlignSeqs = 0;
foreach my $seqID ( $db->getIDs() )
{
unless ( exists $seqNames{$seqID} )
{
$unalignedFastaSeqs .=
">$seqID\n" . $db->getSequence( $seqID ) . "\n";
$unAlignSeqs .=
"Unaligned ( $seqID ): " . $db->getSequence( $seqID ) . "\n";
$numUnAlignSeqs++;
}
}
if ( $numUnAlignSeqs > 0 )
{
print $MOUT "$numUnAlignSeqs sequences could not be aligned to "
. "this reference sequence:\n";
print $MOUT "<PRE>\n$unAlignSeqs\n</PRE>\n";
}
# Find out how many uniq sequences made it into the
# final multiple alignment.
%uniqSeqIDs = ();
foreach my $seqNum ( 0 .. $malign->getNumAlignedSeqs() - 1 )
{
$uniqSeqIDs{ $malign->getAlignedName( $seqNum ) } = {
consStart => $malign->getAlignedStart( $seqNum ),
consEnd => $malign->getAlignedEnd( $seqNum )
};
}
# TODO: Get alignment position ( ie. consensus pos ) so we can
# store this in with the final instances.
$finalMultiAlignmentSize = keys( %uniqSeqIDs );
}
#close $MOUT;
} until ( $finalRound == 2 );
my $gaplessCons = $cons;
$gaplessCons =~ s/-//g;
print " - numRounds = $round\n";
print " - Consensus Length = "
. length( $gaplessCons )
. " ( orig = $round1ConsLen )\n";
print " - Avg Kimura Divergence = "
. sprintf( "%0.2f", $avgKDiv ) . "\n";
print
" - Unaligned sequences = $numUnAlignSeqs ( orig = $round1NumUnAlignSeqs )\n";
} else
{
print $CLASS
. "::buildConsensus(): $pathToFastaFile ( $consName ) "
. "didn't have any hsps.\n";
exit;
}
} # if Run stat from first pass
## Testing: Saving out unaligned fasta for experimentation
open OUT, ">unaligned.fa"
or die "Refiner Failed: Could not open unaligned\.fa file!\n";
#my $ff = $cons;
#$ff =~ s/-//g;
#print OUT ">consensus\n$ff\n";
print OUT $unalignedFastaSeqs;
close OUT;
# Adjust identifiers in MultAln
for ( my $i = 0 ; $i < $malign->getNumAlignedSeqs() ; $i++ )
{
my $id = $malign->getAlignedName( $i );
my $dbDesc = $db->getDescription( $id );
# If we are provided a translation system -- do the translation
if ( $dbDesc =~ /^\s*(\S+:)?(\S+):(\d+)-(\d+)\s*.*$/ )
{
my $originAssembly = $1;
my $originSeq = $2;
my $originStart = $3;
my $originEnd = $4;
my $trueStart = $malign->getAlignedSeqStart( $i ) + $originStart;
my $trueEnd = $malign->getAlignedSeqEnd( $i ) + $originStart;
if ( $options{'giToID'}
&& defined $genomeDBToSeqID{$originSeq} )
{
$originSeq = $genomeDBToSeqID{$originSeq};
}
$malign->setAlignedName( $i, $originSeq );
$malign->setAlignedSeqStart( $i, $trueStart );
$malign->setAlignedSeqEnd( $i, $trueEnd );
}
}
$malign->toSTK( filename => "$pathToFastaFile.refiner.stk" );
print " Build Consensus: " . elapsedTime( 0 ) . "\n";
undef @multiSeqs;
return $cons, $finalMultiAlignmentSize, $avgKDiv;
}
##############################################################################
##############################################################################
##-------------------------------------------------------------------------##
##
## Use: my = writeHTMLMultAlign( multAln => $multAlignRef,
## [destination => $filename|$FH],
## [leftFlankingID => 1],
## [rightFlankingID => 1] );
##
##
##
##-------------------------------------------------------------------------##
sub writeHTMLMultAlign
{
my %parameters = @_;
my $method = "writeHTMLMultAlign";
croak $CLASS. "::$method() missing multAln parameter!\n"
if ( !exists $parameters{'multAln'} );
my $mAlign = $parameters{'multAln'};
my $OUT = *STDOUT;
if ( defined $parameters{'destination'} )
{
if ( ref( $parameters{'destination'} ) !~ /GLOB|FileHandle/ )
{
print $CLASS
. "::$method() Opening file "
. $parameters{'destination'} . "\n"
if ( $DEBUG );
open $OUT, $parameters{'destination'}
or die $CLASS
. "::$method: Unable to open "
. "results file: $parameters{'destination'} : $!";
} else
{
$OUT = $parameters{'destination'};
}
}
print $OUT <<"END";
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>Alignments</title>
<style type="text/css">
font.lowQual {
background: #CD5C5C;
}
font.deletion {
background: #FF0000;
}
font.duplication {
background: #0000FF;
}
font.unknown {
background: #FFFF00;
}
font.dupFlank {
background: #C0C0C0;
}
</style>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
</head>
END
# Find max padding.
my $maxLeftLen = 0;
my $maxRightLen = 0;
my $maxQueryEnd = length( $mAlign->getReferenceSeq() );
foreach my $seqNum ( 0 .. $mAlign->getNumAlignedSeqs() - 1 )
{
my $relLeftLen =
length( $mAlign->getLeftFlankingSequence( $seqNum ) ) -
$mAlign->getAlignedStart( $seqNum );
my $relRightLen =
length( $mAlign->getRightFlankingSequence( $seqNum ) ) -
( $maxQueryEnd - $mAlign->getAlignedEnd( $seqNum ) );
$maxLeftLen = $relLeftLen if ( $maxLeftLen < $relLeftLen );
$maxRightLen = $relRightLen if ( $maxRightLen < $relRightLen );
}
## Calculate Del/Dup candidates
my @dupDelCols = ();
if ( $parameters{'printDupDelCols'} == 1 )
{
my $endStartPairs = $mAlign->_getEndStartPairs();
foreach my $pair ( @{$endStartPairs} )
{
if ( abs( $pair->{'refEnd'} - $pair->{'refStart'} ) < 50 )
{
my $adjStart = 0;
my $adjEnd = 0;
my $absStart = $pair->{'refEnd'};
my $absEnd = $pair->{'refStart'};
if ( $pair->{'refEnd'} > $pair->{'refStart'} )
{
$absStart = $pair->{'refStart'};
$absEnd = $pair->{'refEnd'};
}
$adjStart = $mAlign->getAlignPosFromBPPos( $absStart );
$adjEnd = $mAlign->getAlignPosFromBPPos( $absEnd );
print " adjStart = $adjStart adjEnd=$adjEnd\n" if ( $DEBUG );
if ( $pair->{'avgGapWidth'} > 30 )
{
print "Calling a deletion\n";
# Deletion
push @dupDelCols,
{
'start' => $adjStart,
'end' => $adjEnd,
'type' => "deletion"
};
} elsif ( $pair->{'avgGapWidth'} < 0 )
{
# Duplication
print "Calling a duplication\n";
my $flnkStart =
$mAlign->getAlignPosFromBPPos(
$absStart - abs( $pair->{'avgGapWidth'} ) );
my $flnkEnd = $mAlign->getAlignPosFromBPPos( $absStart - 1 );
push @dupDelCols,
{
'start' => $flnkStart,
'end' => $flnkEnd,
'type' => 'dupFlank'
};
push @dupDelCols,
{
'start' => $adjStart,
'end' => $adjEnd,
'type' => "duplication"
};
$flnkStart = $mAlign->getAlignPosFromBPPos( $absEnd + 1 );
$flnkEnd =
$mAlign->getAlignPosFromBPPos(
$absEnd + abs( $pair->{'avgGapWidth'} ) );
push @dupDelCols,
{
'start' => $flnkStart,
'end' => $flnkEnd,
'type' => 'dupFlank'
};
} else
{
# Unknown
print "Calling an Unknown\n";
push @dupDelCols,
{
'start' => $adjStart,
'end' => $adjEnd,
'type' => "unknown"
};
}
}
}
}
## Calculate low scoring columns
my $matrix = SequenceSimilarityMatrix->new();
$matrix->parseFromFile(
"$RepModelConfig::REPEATMODELER_MATRICES_DIR/wublast/nt/comparison.matrix"
);
my $columns;
my $scoreArray;
if ( defined $parameters{'threshold'} )
{
( $columns, $scoreArray ) = $mAlign->getLowScoringAlignmentColumns(
matrix => $matrix,
threshold => $parameters{'threshold'}
);
} else
{
( $columns, $scoreArray ) =
$mAlign->getLowScoringAlignmentColumns( matrix => $matrix );
}
#print "Low scoring columns:\n";
#foreach my $col ( @{$columns} ) {
# print "Col start = " . $col->[0] . " end = " . $col->[1] . "\n";
#}
print $OUT "<PRE>\n";
# Print out scoreArray just for fun
# find the largest/smallest score
my $max = 0;
for ( my $j = 0 ; $j <= $#{$scoreArray} ; $j++ )
{
my $num = sprintf( "%0.1f", $scoreArray->[ $j ] );
$max = length( $num ) if ( $max < length( $num ) );
$scoreArray->[ $j ] = $num;
}
my $numCols = $max;
my @lines = ();
foreach my $num ( @{$scoreArray} )
{
my $paddedNum = ' ' x ( $numCols );
if ( $num != 0 )
{
$paddedNum = ' ' x ( $numCols - length( $num ) ) . $num;
}
for ( my $j = 0 ; $j < $numCols ; $j++ )
{
$lines[ $j ] .= substr( $paddedNum, $j, 1 );
}
}
my $label = "lowQualScore";
my $paddedLabel = $label . " " x ( 30 - length( $label ) );
foreach my $line ( @lines )
{
print $OUT $paddedLabel . ": " . ' ' x ( $maxLeftLen ) . $line . "\n";
}
# First print the consensus sequence
my $lineStart = 0;
my $name = "consensus";
my $namePad = 30 - length( $name );
my $seq =
$mAlign->consensus(
"$RepModelConfig::REPEATMODELER_MATRICES_DIR/linupmatrix" );
print $OUT "<b><i>$name</i></b>"
. ' ' x $namePad . ": "
. ' ' x ( $maxLeftLen )
. "<font color=\"blue\">$seq</font>\n";
my $name = "Reference ( " . $mAlign->getReferenceName() . " )";
my $namePad = 30 - length( $name );
my $seq = $mAlign->getReferenceSeq();
print $OUT "<b><i>$name</i></b>"
. ' ' x $namePad . ": "
. ' ' x ( $maxLeftLen )
. "<font color=\"blue\">$seq</font>\n";
# Now print the reference and the instances.
for ( my $i = 0 ; $i < $mAlign->getNumAlignedSeqs() ; $i++ )
{
$name = $mAlign->getAlignedName( $i );
if ( length( $name ) > 30 )
{
$name = substr( $name, 0, 30 );
}
$namePad = 30 - length( $name );
my $lfSeq = $mAlign->getLeftFlankingSequence( $i );
my $seq .=
' ' x
( $maxLeftLen - ( length( $lfSeq ) - $mAlign->getAlignedStart( $i ) ) );
if ( $parameters{'leftFlankingID'} eq $i - 1 )
{
$seq .= "<font color=\"blue\">" . lc( $lfSeq ) . "</font>";
} else
{
$seq .= lc( $lfSeq );