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Refiner
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Refiner
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#!/usr/bin/perl
##---------------------------------------------------------------------------##
## File:
## @(#) Refiner
## Author:
## Arian Smit <asmit@systemsbiology.org>
## Robert Hubley <rhubley@systemsbiology.org>
## 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.
#*
###############################################################################
=head1 NAME
Refiner - Generate and refine a seed alignment given a set of family instances
=head1 SYNOPSIS
Refiner [-options] <family fasta sequences>
-threads # : The maximum number of threads the program may use.
NOTE: The fasta file should contain only sequence identifiers and sequences.
The fasta description field is currently reserved for RepeatModeler
use at this time.
=head1 DESCRIPTION
This tool was developed to overcome the limitation many multiple sequence
aligners when supplied with highly diverged and fragmented sequences. Given
a set of related instances of TE family this tool:
- Generates an all-vs-all pairwise alignment to identify the sequence
with the minimal distance (best score) to all other sequences.
- A transitive multiple sequence alignment is generated from the pairwise
alignments to this minimally distant copy and a new consensus is drawn.
- If the consensus has changed, the new consensus is realigned to the
instances and the process is repeated until the consensus stabilizes.
The options are:
=over 4
=item -h(elp)
Detailed help
=back
=head1 SEE ALSO
=over 4
RepeatModeler, RepeatMasker
=back
=head1 COPYRIGHT
Copyright 2005-2022 Institute for Systems Biology
=head1 AUTHOR
Robert Hubley <rhubley@systemsbiology.org>
Arian Smit <asmit@systemsbiology.org>
=cut
#
# 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 Pod::Text;
use Data::Dumper;
# RepeatModeler Libraries
use RepModelConfig;
use lib $RepModelConfig::configuration->{'REPEATMASKER_DIR'}->{'value'};
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
#
my $version = $RepModelConfig::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 = ( '-help',
'-debug',
'-noTmp',
'-quiet',
'-giToID=s',
'-name=s',
'-threads=i' );
# Add configuration parameters as additional command-line options
push @opts, RepModelConfig::getCommandLineOptions();
#
# Get the supplied command line options, and set flags
#
my %options = ();
unless ( &GetOptions( \%options, @opts ) ) {
usage();
}
#
# Provide the POD text from this file and
# from the config file by merging them
# together. The heading "CONFIGURATION
# OVERRIDES" provides the insertion point
# for the configuration POD.
#
sub usage {
my $p = Pod::Text->new();
$p->output_fh( *STDOUT );
my $pod_str;
open IN, "<$0"
or die "Could not open self ($0) for generating documentation!";
while ( <IN> ) {
if ( /^=head1\s+CONFIGURATION OVERRIDES\s*$/ ) {
my $c_pod = RepModelConfig::getPOD();
if ( $c_pod ) {
$pod_str .= $_ . $c_pod;
}
}
else {
$pod_str .= $_;
}
}
close IN;
print "$0 - $version\n";
$p->parse_string_document( $pod_str );
exit( 1 );
}
#
# Resolve configuration settings using the following precedence:
# command line first, then environment, followed by config
# file.
#
RepModelConfig::resolveConfiguration( \%options );
my $config = $RepModelConfig::configuration;
my $NCBIBLASTDB_PRGM = $config->{'RMBLAST_DIR'}->{'value'} . "/makeblastdb";
my $RMBLASTN_PRGM = $config->{'RMBLAST_DIR'}->{'value'} . "/rmblastn";
# Print the internal POD documentation if something is missing
if ( $#ARGV == -1 || $options{'help'} ) {
print "No query sequence file indicated\n\n";
usage();
}
$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;
# LTR_retriever has an issue with "|" symbols. For this
# process the seq identifier will be gi-# instead.
$genomeDBToSeqID{"gi-$2"} = $1;
}
}
close IN;
}
#
# Setup the search engines
#
my $srchEngAllVsAll;
my $srchEngOneVsAll;
$srchEngAllVsAll =
NCBIBlastSearchEngine->new( pathToEngine => $RMBLASTN_PRGM );
$srchEngOneVsAll =
NCBIBlastSearchEngine->new( pathToEngine => $RMBLASTN_PRGM );
if ( not defined $srchEngAllVsAll ) {
die "Refiner Failed: Cannot execute $RMBLASTN_PRGM please make "
. "sure you have setup RepeatModeler to use RMBlast by "
. "running the configure script.\n";
}
my $rmblast_version = $srchEngOneVsAll->getVersion();
my $engineHasQueryThreading = 0;
if ( $rmblast_version =~ /(\d+)\.(\d+)\.(\d+)\+/ ) {
my $majorVer = $1;
my $minorVer = $2;
my $revision = $3;
if ( $majorVer > 2 || ($majorVer == 2 && $minorVer >= 13 )) {
$engineHasQueryThreading = 1;
}
}
#
# 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 ( $DEBUG );
#
# Handle one sequence case
#
open IN, "<$file" or die "Could not open $file for reading!";
my $firstSeq;
my $firstID;
my $count = 0;
while ( <IN> ) {
if ( /^>(\S+)/ ) {
$count++;
last if ( $count > 1 );
$firstID = $1;
next;
}
s/[\n\r\s]+//g;
$firstSeq .= uc($_);
}
close IN;
# Name the final consensus sequence
my $id = "family";
$id = $options{'name'} if ( $options{'name'} );
my $cons;
my $maSize;
my $avgKDiv;
if ( $count > 1 ) {
( $cons, $maSize, $avgKDiv ) =
&buildConsensus( "$FindBin::RealBin/Matrices",
$srchEngAllVsAll, $srchEngOneVsAll, $file, $tmpDir );
}
else {
my $malign = MultAln->new( sequences => [ [ $firstID, $firstSeq ] ] );
$cons = $malign->consensus();
$maSize = 1;
$avgKDiv = 0;
my $db = FastaDB->new( fileName => $file,
openMode => SeqDBI::ReadOnly );
adjustIdentifiers($malign, $db);
$malign->toSTK( filename => "$file.refiner.stk", id => $id );
}
$cons =~ s/-//g;
open OUTC, ">$file.refiner_cons";
# Save the consensus to the consensi file.
print OUTC ">$id ( Final Multiple Alignment Size = " . $maSize
. " , Avg Kimura = $avgKDiv )\n";
print OUTC "$cons\n";
close OUTC;
}
##########################################################################
##########################################################################
##########################################################################
##########################################################################
sub buildConsensus {
my $matrixDir = 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 );
$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 "========================="
. $consName
. "=========================\n";
print " -------------------ROUND 1 ------------------ \n";
}
# MAKEBLASTDB the database
system( "$NCBIBLASTDB_PRGM -blastdb_version 4 -out $pathToFastaFile "
. "-dbtype nucl -in $pathToFastaFile >> "
. "$wrkDir/makeblastdb.log 2>&1" );
## Setup the ALL vs ALL parameters
$srchEngAllVsAll->setMatrix( "$matrixDir/ncbi/nt/comparison.matrix" );
$srchEngAllVsAll->setMinScore( 150 );
$srchEngAllVsAll->setGenerateAlignments( 1 );
$srchEngAllVsAll->setGapInit( -25 );
$srchEngAllVsAll->setInsGapExt( -5 );
$srchEngAllVsAll->setDelGapExt( -5 );
$srchEngAllVsAll->setMinMatch( 7 );
$srchEngAllVsAll->setCores( $options{'threads'} ? $options{'threads'} : undef );
#$srchEngAllVsAll->setBandwidth( -50 );
$srchEngAllVsAll->setTempDir( dirname( $pathToFastaFile ) );
$srchEngAllVsAll->setScoreMode( SearchEngineI::complexityAdjustedScoreMode );
## Setup the ONE vs ALL parameters
$srchEngOneVsAll->setMatrix( "$matrixDir/ncbi/nt/comparison.matrix" );
$srchEngOneVsAll->setMinScore( 150 );
$srchEngOneVsAll->setGenerateAlignments( 1 );
$srchEngOneVsAll->setGapInit( -25 );
$srchEngOneVsAll->setInsGapExt( -5 );
$srchEngOneVsAll->setDelGapExt( -5 );
$srchEngOneVsAll->setMinMatch( 7 );
$srchEngOneVsAll->setCores( $options{'threads'} ? $options{'threads'} : undef);
$srchEngOneVsAll->setTempDir( dirname( $pathToFastaFile ) );
$srchEngOneVsAll->setScoreMode( SearchEngineI::complexityAdjustedScoreMode );
$srchEngOneVsAll->setMaskLevel( 80 );
# 1. Search all instances against each other
$srchEngAllVsAll->setQuery( $pathToFastaFile );
$srchEngAllVsAll->setSubject( $pathToFastaFile );
print $CLASS
. "::buildConsensus(): Running All-vs-All "
. "on $pathToFastaFile \n"
if ( $DEBUG );
my $round = "1";
print "Params: " . $srchEngAllVsAll->getParameters() . "\n"
if ( $DEBUG );
my ( $runStat, $familyCollection ) = $srchEngAllVsAll->search();
print "Search complete\n" if ( $DEBUG );
## Cleanup after run
# 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 => $familyCollection );
##
## Prototype
##
#if ( 1 ) {
# print "#\n";
# print "# PROTOTYPE: running Tensor Sketch to caculate distances...\n";
# print "#\n";
# system("$FindBin::RealBin/sketch --tuple_length 3 --embed_dim 16 --window_size 30 --stride 3 --alphabet dna5 -i $pathToFastaFile -o $wrkDir/sketch-dist.tsv >& /dev/null");
# open TSS,"<$wrkDir/sketch-dist.tsv" or die "Could not open $wrkDir/sketch-dist.tsv\n";
# my %tssSumDistsHash = ();
# my @tssSumDistsArray = ();
# while ( <TSS> ){
# if ( /^(\S+)\s+([\d\.]+)/ ) {
# push @tssSumDistsArray, [$1,$2];
# $tssSumDistsHash{$1} = $2;
# }
# }
# close TSS;
# @tssSumDistsArray = sort { $a->[1] <=> $b->[1] } @tssSumDistsArray;
# print "# Ten lowest sum distances according to TSS:\n";
# my $inTop = 0;
# for ( my $l = 0; $l < 5; $l++ ) {
# print "# " . $tssSumDistsArray[$l]->[0] . " " . $tssSumDistsArray[$l]->[1] . "\n";
# $inTop = 1 if ( $tssSumDistsArray[$l]->[0] eq $refID );
# }
# print "#\n";
# print "# Highest scoring sequence according to blast: $refID\n";
# print "#\n";
# #print "# Overriding refID with TSS result\n";
# #$refID = $tssSumDistsArray[0]->[0];
#}
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 => $db,
maxFlankingSequenceLen => -1
);
# 20190605: We do want to include the reference in round-1 because it's
# a real input sequence. Also, matrix was unused here.
#$cons = $malign->consensus( "$matrixDir/linupmatrix" );
$cons = $malign->consensus( inclRef => 1 );
my (
$leftMostSequence, $leftMostSequenceID,
$rightMostSequence, $rightMostSequenceID
)
= &getLongestFlankingExtension( multAln => $malign );
writeHTMLMultAlign(
multAln => $malign,
inclRef => 1,
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;
my $sumScore = 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 = "";
$rightMostSequence = "";
# MAKEBLASTDB the database
#. "-parse_seqids -dbtype nucl -in "
system( "$NCBIBLASTDB_PRGM -blastdb_version 4 -out "
. "$wrkDir/$consName-cons-$round.fa "
. "-dbtype nucl -in "
. "$wrkDir/$consName-cons-$round.fa >> "
. "$wrkDir/makeblastdb.log 2>&1" );
# Setup the search parameters
# TODO: Get version of RMBLAST if 2.13+ use mt_mode=1
if ( $engineHasQueryThreading ) {
$srchEngOneVsAll->setThreadByQuery(1);
}
$srchEngOneVsAll->setSubject( "$wrkDir/$consName-cons-$round.fa" );
$srchEngOneVsAll->setQuery( $pathToFastaFile );
print $CLASS
. "::buildConsensus(): Cons-vs-All "
. "$consName\n"
if ( $DEBUG );
print "Params: " . $srchEngOneVsAll->getParameters() . "\n"
if ( $DEBUG );
( $runStat, $familyCollection ) = $srchEngOneVsAll->search();
# Remove the ncbi databases
system( "rm $wrkDir/$consName-cons-$round.fa.n*" ) unless ( $DEBUG );
print $CLASS
. "::buildConsensus(): RMBlast 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;
$sumScore = 0;
for ( my $j = 0 ; $j < $familyCollection->size() ; $j++ ) {
# Testing
#print "OUT: "
# . $familyCollection->get( $j )
# ->toStringFormatted( SearchResult::AlignWithQuerySeq ) . "\n";
my $qryID = $familyCollection->get( $j )->getQueryName();
$sumScore += $familyCollection->get( $j )->getScore();
$seqNames{$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 " - sumScore = $sumScore\n";
unless ( $options{'quiet'} ) {
print " - numRounds = $round\n";
print " - sumScore = $sumScore\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 {
if ( $DEBUG ) {
print $CLASS
. "::buildConsensus(): $pathToFastaFile ( $consName ) "
. "didn't have any hsps.\n";
}else{
print " Refiner: Family $consName didn't produce 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";
#print OUT $unalignedFastaSeqs;
#close OUT;
adjustIdentifiers($malign, $db);
#$malign->toSTK( filename => "$pathToFastaFile.refiner.stk", includeTemplate => 1, nuclRF => 1 );
$malign->toSTK( filename => "$pathToFastaFile.refiner.stk" );
print " Build Consensus: " . elapsedTime( 0 ) . "\n"
unless ( $options{'quiet'} );
undef @multiSeqs;
return $cons, $finalMultiAlignmentSize, $avgKDiv;
}
sub adjustIdentifiers {
my $malign = shift;
my $db = shift;
# Adjust identifiers in MultAln
my %onlyUniq;
# 01/31/22: RMH - This "delete in forward iteration" error causes
# some sequences to retain the 'gi|#' identifier
# rather than being correctly translated back to
# genomic identifiers.
#for ( my $i = 0 ; $i < $malign->getNumAlignedSeqs() ; $i++ ) {
for ( my $i = $malign->getNumAlignedSeqs()-1; $i >= 0 ; $i-- ) {
my $id = $malign->getAlignedName( $i );
my $dbDesc = $db->getDescription( $id );
my $refOrient = $malign->getAlignedOrientation( $i );
# If we are provided a translation system -- do the translation
# e.g hg38:chr1:300-400
# or
# chr1:300-400
# gi|1:300-400
# gi-1:300-400
# gi-1:300..400
#
my $assembly;
my $seqID;
my $start;
my $end;
if ( $dbDesc =~ /^\s*(\S+:)?(\S+):(\d+)-(\d+)\s*.*$/ ) {
$assembly = $1;
$seqID = $2;
$start = $3;
$end = $4;
# LTR Retriever prints out stuff like this:
# gi-1:11224114..11230723_INT#LTR/Gypsy
}
elsif ( $id =~ /^\s*(\S+):(\d+)\.\.(\d+)/ ) {
$seqID = $1;
$start = $2;
$end = $3;
}else {
# We don't have a recognizable identifier
$seqID = $id;
}
if ( $seqID && $start && $end ) {
if ( $options{'giToID'}
&& exists $genomeDBToSeqID{$seqID} )
{
$seqID = $genomeDBToSeqID{$seqID};
}
$malign->setAlignedName( $i, $seqID );
my $adjStart;
my $adjEnd;
#if ( $end < $start ) {
# $malign->setAlignedOrientation( $i, "-" );
# $adjStart = $malign->getAlignedSeqStart( $i ) + $end - 1;
# $adjEnd = $malign->getAlignedSeqEnd( $i ) + $end - 1;
#}
#else {
# $adjStart = $malign->getAlignedSeqStart( $i ) + $start - 1;
# $adjEnd = $malign->getAlignedSeqEnd( $i ) + $start - 1;
#}
# 2/1/22: RMH - Fixed a bug with coordinate translation. The
# coordinates stored in the Family-#.fa file
# are one-based, fully-closed. They are also
# stored in reversed order if the sequence
# is reverse complemented. In the above code
# we added the coordinates to the end position
# rather than subtracting them from the start!
if ( $end < $start ) {
if ( $refOrient eq "C" || $refOrient eq "-" ) {
$malign->setAlignedOrientation( $i, "+" );
}else{
$malign->setAlignedOrientation( $i, "-" );
}
# AlignedStart is always lower than AlignedEnd in the MALIGN obj
$adjEnd = $start - $malign->getAlignedSeqStart( $i ) + 1;
$adjStart = $start - $malign->getAlignedSeqEnd( $i ) + 1;
}
else {
if ( $refOrient eq "C" || $refOrient eq "-" ) {
$malign->setAlignedOrientation( $i, "-" );
}else{
$malign->setAlignedOrientation( $i, "+" );
}
$adjStart = $start + $malign->getAlignedSeqStart( $i ) - 1;
$adjEnd = $start + $malign->getAlignedSeqEnd( $i ) - 1;
}
$malign->setAlignedSeqStart( $i, $adjStart );
$malign->setAlignedSeqEnd( $i, $adjEnd );
}
elsif ( $dbDesc ) {
warn "Could not parse identifier: $dbDesc\n";
}
my $finalID = "$seqID:" . $malign->getAlignedSeqStart( $i ) . "-" . $malign->getAlignedSeqEnd( $i );
if ( exists $onlyUniq{$finalID} ) {
# TODO: make this an function of MultAln
splice(@{ $malign->{'alignCol'} }, $i+1, 1);
}
$onlyUniq{$finalID} = 1;
}
}
##############################################################################
##############################################################################
##-------------------------------------------------------------------------##
##
## 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 $inclRef = 0;
if ( defined $parameters{'inclRef'} ) {
$inclRef = 1;
}
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 ) {