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RepeatClassifier
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#!/u1/local/bin/perl
##---------------------------------------------------------------------------##
## File:
## @(#) RepeatClassifier
## Author:
## Arian Smit <[email protected]>
## Robert Hubley <[email protected]>
## Description:
## Given a set of repeat models, and some hand crafted databases,
## this script attempts to classify the models. The classification
## is compatable with the RepeatMasker program.
##
#******************************************************************************
#* 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: RepeatClassifier,v $
# Revision 1.29 2017/04/04 23:57:12 rhubley
# - Nearing a release
#
# Revision 1.28 2017/03/31 17:25:39 rhubley
# - Lots-o-improvements. Starting preparation for release.
#
# Revision 1.27 2014/05/08 19:38:00 rhubley
# - Added -pa option and parallelized the blast all-vs-other searches
#
# Revision 1.26 2013/10/28 23:01:07 rhubley
# - Updates
#
# Revision 1.25 2012/08/22 18:46:24 rhubley
# -- a refresh checkin and adding a new utility
#
# Revision 1.24 2010/06/11 23:45:30 rhubley
# -- Getting ready for a release
#
# Revision 1.23 2010/06/10 18:15:44 rhubley
# - Fixed a bug that Arian found with RepeatScout models refined by the
# RMBLAST engine. The problem had to do with a rev/compl operation
# in BuildRSConsensi
#
# - Readying RepeatModeler for release with RMBLAST
#
# Revision 1.22 2010/06/04 22:55:18 rhubley
# - Some bug fixes.
# - Changes to support rmblast package
#
# Revision 1.21 2009/03/26 17:32:01 rhubley
# - Fixed stupid Debian/Ubuntu choice of using DASH as /bin/sh.
#
# Revision 1.20 2008/05/01 22:09:59 rhubley
# - Merged the libraries and placed in RepeatMasker distribution
#
# Revision 1.19 2008/04/28 17:02:26 rhubley
# - Fixed temp directory problems repoted by Hans-Rudolf Hotz at Sanger
#
# Revision 1.18 2008/04/16 18:29:33 rhubley
# - Refinements of the RS instance collection mechanism
# - Refinements of the masking mechanism. May switch to using
# RM for this step.
# - Found a few more hard coded directory dependencies
#
# Revision 1.17 2008/03/27 19:55:08 rhubley
# - Refining the output messages
# - RepeatPeps distributed with this release
# - Configure now builds wublast libraries during installation
#
# Revision 1.16 2008/03/25 22:48:29 rhubley
# - Removed all debuging output and cleaned up RepeatModeler's
# parameter settings.
#
# Revision 1.15 2008/03/25 21:29:47 rhubley
# - Recent updates include
# - Fixes to RepeatClassifier
# - Addition of RepeatScout
#
# Revision 1.14 2008/01/24 22:11:34 rhubley
# - Starting fresh 1/1/24
#
# Revision 1.13 2006/07/07 22:11:05 rhubley
# - general update to MultAln.pm
#
# Revision 1.12 2005/04/12 17:55:32 rhubley
# - Misc changes. Moved allpeps library out to RepeatMasker
#
# Revision 1.11 2005/03/17 22:04:02 rhubley
# Silenced the XDFORMAT program
#
# Revision 1.10 2005/03/16 22:55:37 rhubley
# - Clean up
#
# Revision 1.9 2005/03/16 19:53:14 rhubley
# - Last minute changes
#
# Revision 1.8 2005/03/16 01:38:35 rhubley
# - Fixed a few bugs in RepeatClassifier
#
# Revision 1.7 2005/03/12 00:44:06 rhubley
# - Misc
#
# Revision 1.6 2005/03/11 23:42:37 rhubley
# - Tidying et al
#
# Revision 1.5 2005/03/11 20:49:09 rhubley
# - New master configuration file
#
# Revision 1.4 2005/03/11 00:29:53 rhubley
# - Ran perltidy and added some more info output
#
# Revision 1.3 2005/03/10 23:26:58 rhubley
# - Working my way to the first release
#
# Revision 1.2 2005/03/08 19:35:30 rhubley
# - Incorporated name sanitizing into buildXDFDatabase.pl
# - RepeatModeler can now change it's family minimum size
# - Added buildXDFDatabase to Makefile
#
# Revision 1.1 2005/03/07 22:32:53 rhubley
# - Initial checkn's of some modules
# - See lab notebook
#
###############################################################################
#
# To Do:
#
#
=head1 NAME
RepeatClassifier - Classify Repeat Models
=head1 SYNOPSIS
RepeatClassifier [-options] -consensi <repeat model file>
[-stockholm <stockholm file>]
[-engine <abblast|ncbi>]
=head1 DESCRIPTION
The options are:
=over 4
=item -h(elp)
Detailed help
=back
=head1 SEE ALSO
=over 4
RepeatModeler
=back
=head1 COPYRIGHT
Copyright 2005-2010 Institute for Systems Biology
=head1 AUTHOR
Robert Hubley <[email protected]>
=cut
#
# Module Dependence
#
use strict;
use FindBin;
use lib $FindBin::RealBin;
use Data::Dumper;
use Cwd;
use Carp;
use File::Basename;
use Getopt::Long;
# RepeatModeler Libraries
use RepModelConfig;
use lib $RepModelConfig::REPEATMASKER_DIR;
use RepeatUtil;
# RepeatMasker Libraries
use WUBlastSearchEngine;
use NCBIBlastSearchEngine;
use SearchResult;
use SearchResultCollection;
use SeqDBI;
use FastaDB;
use SeedAlignmentCollection;
use SeedAlignment;
#
# Class Globals & Constants
#
my $CLASS = "RepeatClassifier";
my $DEBUG = 0;
$DEBUG = 1 if ( $RepModelConfig::DEBUGALL == 1 );
#
# Version
# -- NOTE: This is filled in by configure
my $version = "#VERSION#";
$version = "DEV" if ( $version =~ /\#VERSION\#/ );
#
# Option processing
# e.g.
# -t: Single letter binary option
# -t=s: String parameters
# -t=i: Number paramters
#
my @opts = qw( help consensi=s engine=s stockholm=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 ( !defined $options{'consensi'} || ! -s $options{'consensi'} || $options{'help'} ) {
print "No database indicated or it is an empty file.\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;
}
die $CLASS . ": Cannot run classification on an empty consensus file!\n"
if ( -z $options{'consensi'} );
#
# Setup the search engine
#
my $searchEngineN;
my $engine = $RepModelConfig::DEFAULT_SEARCH_ENGINE;
$engine = $options{'engine'} if ( $options{'engine'} );
if ( $engine )
{
if ( $engine =~ /wublast|abblast/i )
{
$engine = "abblast";
$searchEngineN = WUBlastSearchEngine->new(
pathToEngine => $RepModelConfig::WUBLASTN_PRGM );
if ( not defined $searchEngineN )
{
die "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";
$searchEngineN = NCBIBlastSearchEngine->new(
pathToEngine => $RepModelConfig::RMBLASTN_PRGM );
if ( not defined $searchEngineN )
{
die "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;
}
}
#
# Print greeting
#
print "RepeatClassifier Version $version\n";
print "===============================\n";
print "Search Engine = $engine\n";
if ( $DEBUG )
{
print "\nRepeatClassifier run as: $0 " . join( @ARGV ) . "\n";
print "Current Working Directory: " . getcwd() . "\n";
print "Perl Version: $]\n\n";
}
my $cmdSuffix = "> /dev/null 2>&1";
$cmdSuffix = "" if ( $DEBUG );
#-------------------------------------------------------------------------##
#
# Step 1: Simple repeat / low complexity identification
#
# Before any comparison, identify simple-repetitive DNA that sneaked
# through.
#
# We currently use TRF and RepeatMasker to scan for low_complexity and
# and tandem repeats.
#
print " - Looking for Simple and Low Complexity sequences..\n";
system( "cp $options{'consensi'} tmpConsensi.fa" );
my $cmd = "$RepModelConfig::REPEATMODELER_DIR/TRFMask tmpConsensi.fa "
."$cmdSuffix";
print "Running: $cmd\n" if ( $DEBUG );
system( $cmd );
if ( ! -s "tmpConsensi.fa.masked" )
{
die "Something went wrong with the TRFMask program. The tmpConsensi.fa.masked file was missing or empty!\n";
}
system("mv tmpConsensi.fa.masked tmpConsensi.fa");
$cmd = "$RepModelConfig::REPEATMASKER_DIR/RepeatMasker -qq -noint "
."-no_is tmpConsensi.fa $cmdSuffix";
print "Running: $cmd\n" if ( $DEBUG );
system( $cmd );
system( "mv tmpConsensi.fa $options{'consensi'}.masked" );
if ( ! -s "$options{'consensi'}.masked" )
{
die "Something went wrong with the RepeatMasker program. The "
."$options{'consensi'}.masked file is missing or empty\n";
}
# Those sequences longer than 50 bp that have no consecutive strings
# of unmasked bases >= 50 bp left should be marked as potential
# tandem/simple/segmental duplication type repeats. If they don't
# hit anything significant in the blastx comparison then remove
# them and only put them back if we can mark them as tandem with
# a specific base consensus pattern.
my $maskedDB = FastaDB->new( fileName => "$options{'consensi'}.masked",
openMode => SeqDBI::ReadOnly );
my %simpleRepeats = ();
foreach my $seqID ( $maskedDB->getIDs() )
{
my $seq = $maskedDB->getSequence( $seqID );
$seq =~ s/[Nn]+/\#/g;
my $numAmbig = ($seq =~ tr/\#/\#/);
if ( ( $numAmbig / length( $seq ) ) > 0.8 )
{
warn "Consensus $seqID is >80% ambiguous sequence after masking!\n"
if ( $DEBUG );
$simpleRepeats{ $seqID }++;
}
}
###### TODO
# Selfcomparison of this file should reveal if we're dealing with a
# satellite that needs to be included: if the sequence matches (much)
# higher to itself, given a shift, than to the consensus simple repeat
# string, there is bound to be a satellite here.
#
# We can also just run TRF on the entire consensus sequence database
# to see if a satellite consensus has been build. It is possible that
# individual copies may have been too diverged to detect as such.
# I don't know if new satellites will come out of this, but it's worth a try.
######
#-------------------------------------------------------------------------##
#
# Step 2: comparison against database of transposon proteins
#
# wublastx the simple-masked consensi vs the transposable element
# protein database with the fasta line format
# >TWIFBIG#DNA/HAT-Ac
# This name may be *immediately* followed by #ReverseORF to indicate
# that the product is encoded on the opposite strand of the
# transposable element. It needs to be right after it, otherwise it
# may fall on the next line in the blastx output's hit description.
#
# RepModelConfig::WUBLASTX_PRGM parameters default with -W 2
# Originally I had: -filter xnu -wordmask seg
# but the masking of simple repeats and low_complexity at the DNA
# level seems better (more real matches reported)
print " - Looking for similarity to known repeat proteins..\n";
#determines which matches above which P value will be ignored
my $cutoffP = 0.001;
# keeps only those matches not overlapped by > $masklevel % by matches
# with a better p value
# $masklevel 101 does not exist (same as masklevel 100)
my $masklevel = 80;
# initialize the search
my $blastCmd;
if ( $engine eq "abblast" )
{
if ( ! -s "$RepModelConfig::REPEATMASKER_DIR/Libraries/RepeatPeps.lib.xps" )
{
die "Missing $RepModelConfig::REPEATMASKER_DIR/Libraries/"
."RepeatPeps.lib.xps!\n"
."Please rerun the configure program in the RepeatModeler directory\n"
."before running this script.\n";
}
# Setup the matrix directory so that wublast can find Blossom62
$ENV{BLASTMAT} = "$RepModelConfig::WUBLAST_DIR/matrix";
$ENV{WUBLASTMAT} = $ENV{BLASTMAT};
$blastCmd = "$RepModelConfig::WUBLASTX_PRGM " .
"$RepModelConfig::REPEATMASKER_DIR/Libraries/RepeatPeps.lib " .
"$options{'consensi'}.masked -W 2 > tmpBlastXResults.out 2>&1";
print " + Running abblastx vs RepeatPeps.lib...\n" if ( $DEBUG );
}elsif ( $engine eq "ncbi" )
{
if ( ! -s "$RepModelConfig::REPEATMASKER_DIR/Libraries/RepeatPeps.lib.psq" )
{
die "Missing $RepModelConfig::REPEATMASKER_DIR/Libraries/"
."RepeatPeps.lib.psq!\n"
."Please rerun the configure program in the RepeatModeler directory\n"
."before running this script.\n";
}
$blastCmd = "$RepModelConfig::NCBIBLASTX_PRGM " .
"-db $RepModelConfig::REPEATMASKER_DIR/Libraries/RepeatPeps.lib " .
"-query $options{'consensi'}.masked -word_size 2 > tmpBlastXResults.out 2>&1";
print " + Running rmblastx vs RepeatPeps.lib...\n" if ( $DEBUG );
}
print " o Running: $blastCmd\n" if ( $DEBUG );
system( $blastCmd );
if ( ! -s "tmpBlastXResults.out" )
{
die "Something went wrong while running blastX. The tmpBlastXResults.out"
." file was missing or is empty\n";
}
# Reads in the blastx output
# creates %pval; rest is written to files
my $blastXResults = &wublastxanalysis(
fileName => "tmpBlastXResults.out",
pValueCutoff => $cutoffP,
#seqDB => $consDB,
masklevel => $masklevel
);
# This leaves us with a modified fasta file (some classified, even
# fewer orientation adjusted based on blastx comparison), which is
# next compared to RepeatMasker.lib.
#-------------------------------------------------------------------------##
#
# Step 3: comparison against RepeatMasker.lib
#
# Use the comparison (?) matrix (the symmetrical one, with the same
# gaps (-25 -5, I believe) as you're using in element comparison
# Cutoff needs to be high enough to avoid false labels, but low enough
# to see distant matches to SINEs, for example. So, 250 sounds good.
#
# One strategy (unexplored as yet) could be to do this in two
# steps. First have a minimum score of, say, 350, that guarantees
# significance. This will avoid many matches that cause conflicts in
# annnotation and so much headache in the following code Then take all
# the unclassified repeats (#Unknown) and check with minimum score 225
# and a smaller minmatch.
print " - Looking for similarity to known repeat consensi..\n";
$searchEngineN->setTempDir( dirname( $options{'consensi'} ) );
$searchEngineN->setMinScore( 250 );
$searchEngineN->setGenerateAlignments( 0 );
$searchEngineN->setGapInit( -25 );
$searchEngineN->setInsGapExt( -5 );
$searchEngineN->setDelGapExt( -5 );
$searchEngineN->setMinMatch( 7 );
$searchEngineN->setUseDustSeg( 0 );
$searchEngineN->setScoreMode( SearchEngineI::complexityAdjustedScoreMode );
$searchEngineN->setQuery( $options{'consensi'} );
if ( $engine eq "abblast" )
{
$searchEngineN->setMatrix(
"$RepModelConfig::REPEATMODELER_MATRICES_DIR/wublast/nt/comparison.matrix" );
if ( ! -s "$RepModelConfig::REPEATMASKER_DIR/Libraries/RepeatMasker.lib.xns" )
{
die "Missing $RepModelConfig::REPEATMASKER_DIR/Libraries/"
."RepeatMasker.lib.xns!\nPlease rerun the configure program "
."in the RepeatModeler directory\nbefore running this script.\n";
}
$searchEngineN->setAdditionalParameters( " -gapW=32" );
}else {
$searchEngineN->setMatrix(
"$RepModelConfig::REPEATMODELER_MATRICES_DIR/ncbi/nt/comparison.matrix"
);
if ( ! -s "$RepModelConfig::REPEATMASKER_DIR/Libraries/RepeatMasker.lib.nsq" )
{
die "Missing $RepModelConfig::REPEATMASKER_DIR/Libraries/"
."RepeatMasker.lib.nsq!\nPlease rerun the configure program "
."in the RepeatModeler directory\nbefore running this script.\n";
}
}
$searchEngineN->setSubject(
"$RepModelConfig::REPEATMASKER_DIR/Libraries/RepeatMasker.lib" );
print " + Running blastn vs RepeatMasker.lib...\n" if ( $DEBUG );
my ( $status, $searchResultCol ) = $searchEngineN->search();
if ( $status ) {
die $CLASS . ": ERROR from search engine (", $? >> 8, ") \n";
}
my ( $classref, $oriref ) = &vsRMlibAnalysis( searchResults => $searchResultCol,
blastXResults => $blastXResults );
print "DUMPER: classref = \n" . Dumper( $classref ) . "\n" if ( $DEBUG );
print "DUMPER blastXResults = \n" . Dumper( $blastXResults ) . "\n" if ( $DEBUG );
# reads in, at the moment, a modified cross_match file similar to the
# repeatmasker .out file having "+" for forward strand matches so that
# all lines have the same number of columns, but it does not have the
# query and subject names split on #
# Obviously to be replaced by your reader.
# print out the new modifications
# I suspect I could have used one subroutine to do this for both the
# comparison against the proteins and against the repeatmasker.lib ,
# but I incorporated the printing in step2 in a different way.
&changeconsensusfastafile( $classref, $oriref, \%simpleRepeats,
$options{'consensi'},
"$options{'consensi'}.classified" );
my $stkFilePrefix = $options{'stockholm'};
$stkFilePrefix =~ s/^(\S+)\.stk$/$1/;
&changeStockholmFile($classref, $oriref, \%simpleRepeats,
$options{'stockholm'},
"$stkFilePrefix-classified.stk" );
# Output is a further classified and oriented fasta file of consensus sequences
# TODO:
# step 4: blastx comparison of complexity masked consensi vs nr
# put aside all consensus sequences that
# 1) don't match anything in transposon protein database and
# 2) don't match anything in repeatmasker library and
# 3) have a very clear match to a protein in nr database (p < 10-6)
# 4) and the description line of the protein matched does not contain
# the strings:
# transpos, retrovir, retroelement, reverse transcri, ribonuclease H,
# envelope, endonuclease, helicase, replicase, insertion sequence,
# insertion element, recombinase, rolling circle
# Also put aside when
# match to nr protein p < 10-10 (much room to tweak)
# 2) and 4) are true
# the best p value against the transposon protein database is > 10-6,
# or
# match to nr protein p < 10-8
# 1) and 4) are true
# highest score vs repeatmasker library < 400
## No code yet!
# remember to add:
# wu-blast of final consensus seqs against reverse, non-complimented
# random genome batch to catch false positives
unlink "tmpBlastXResults.out" if ( !$DEBUG && -e "tmpBlastXResults.out" );
unlink "tmpBlastXResults.out.bxsummary"
if ( !$DEBUG && -e "tmpBlastXResults.out.bxsummary" );
unlink "tmpConsensi.fa.cat" if ( !$DEBUG && -e "tmpConsensi.fa.cat" );
unlink "tmpConsensi.fa.log" if ( !$DEBUG && -e "tmpConsensi.fa.log" );
unlink "tmpConsensi.fa.masked" if ( !$DEBUG && -e "tmpConsensi.fa.masked" );
unlink "tmpConsensi.fa.out" if ( !$DEBUG && -e "tmpConsensi.fa.out" );
unlink "tmpConsensi.fa.tbl" if ( !$DEBUG && -e "tmpConsensi.fa.tbl" );
#unlink "tempoutfile" if ( !$DEBUG && -e "tempoutfile" );
#unlink "consensi.fa.masked" if ( !$DEBUG && -e "consensi.fa.masked" );
# Cya!
exit;
#-------------------- S U B R O U T I N E S ------------------------------#
##---------------------------------------------------------------------##
## Use: my $pValuesRef = &wublastxanalysis( fileName => "",
## pValueCutoff => #,
## seqDB => SeqDBI,
## masklevel => # );
##
## fileName : Reads in a wublastx results file, interprets
## matches and creates a semi-classified "tempoutfile".
##
## Returns
##
##
##---------------------------------------------------------------------##
sub wublastxanalysis {
my %parameters = @_;
# Result file
die $CLASS . "::wublastxanalysis(): Bad or missing fileName parameter!"
if ( !defined $parameters{'fileName'} || !-s $parameters{'fileName'} );
my $summaryfile = $parameters{'fileName'} . ".bxsummary";
open BXTP, "<$parameters{'fileName'}"
|| die $CLASS
. "::wublastxanalysis(): Could not open file $parameters{'fileName'}!\n";
die $CLASS . "::wublastxanalysis(): Missing pValueCutoff parameter!"
if ( !defined $parameters{'pValueCutoff'} );
die $CLASS . "::wublastxanalysis(): Missing output parameter!"
if ( !defined $parameters{'masklevel'} );
my $masklevel = $parameters{'masklevel'};
my $cutoffP = $parameters{'pValueCutoff'};
# Result datastructure which stores all the subject hits
# for a given query
#
# $queryHits{ subjectID } -> { 'beg' => #,
# 'end' => #,
# 'or' => "Minus",
# 'p' => #,
# 'score' => #,
# 'identical' => #,
# 'aligned' => #,
# 'positives' => # };
# $queryHits{ 'query' }
# $queryHits{ 'oppositestrand' }
#
my %bxResults = ();
my %queryHits = ();
my %pValues = ();
my $on;
my $orientation;
my $sbjct;
open SUMR, ">$summaryfile";
#
# Read in blastx results and for each queryHitSet call
# "chooseBestBlastX".
#
while ( <BXTP> ) {
chomp;
if ( /^Query=\s+(\S+)/ ) {
if ( defined $queryHits{'query'} )
{
my ( $class, $orient, $pVal ) =
&chooseBestBlastX(
queryHits => \%queryHits,
pValues => \%pValues,
masklevel => $masklevel
);
$bxResults{ $queryHits{'query'} } = { 'class' => $class,
'orient' => $orient,
'pVal' => $pVal };
}
%queryHits = ();
$queryHits{'query'} = $1;
$on = 1;
$sbjct = "";
}
elsif ( /^>\s*(\S+)/ ) {
# ab/ncbi blastx
$sbjct = $1;
if ( /\#ReverseORF/ ) {
$queryHits{'oppositestrand'} = 1;
}
else {
$queryHits{'oppositestrand'} = 0;
}
}
elsif ( /Frame\s*=\s*([-+])(\d+)/ )
{
# ncbi/ab blastx
$orientation = $1;
$orientation = "Plus" if ( $orientation eq "+" );
$orientation = "Minus" if ( $orientation eq "-" );
}
if ( /^ Score\s*=\s*([\d\.]+) .+ Expect(?:\(\d+\))? = (\S+)/ ) {
# ncbi/ab blastx
# NOTE: The PValue and EValue are essentially identical
# values below 0.001
if ( $2 <= $cutoffP ) {
if ( defined $queryHits{$sbjct} ) {
$queryHits{$sbjct}->{'score'} = $1
unless $queryHits{$sbjct}->{'score'} > $1;
$queryHits{$sbjct}->{'p'} = $2
unless $queryHits{$sbjct}->{'p'} < $2;
}
else {
$queryHits{$sbjct}->{'score'} = $1;
$queryHits{$sbjct}->{'p'} = $2;
}
$queryHits{$sbjct}->{'or'} = $orientation;
$on = 1;
}
else {
$on = 0;
# this and subsequent matches have a P value too high
# to consider
}
}
elsif ( $on && /^ Identities = (\d+)\/(\d+).+ Positives = (\d+)/ ) {
# ncbi/ab blastx
$queryHits{$sbjct}->{'identical'} += $1;
$queryHits{$sbjct}->{'aligned'} += $2;
$queryHits{$sbjct}->{'positives'} += $3;
# we could consider extracting the number of Xs in the
# aligned portions of both the query and sbjct these can
# be subtracted from the mismatches to give a maximum
# identity and similarity. Currently an underestimate is
# given; calculation would involve checking for Xs
# opposite gaps though, so not so straight forward
}
elsif ( $on && /^Query:?\s+(\d+).*\s(\d+)\s*$/ ) {
# ncbi/ab blastx
my $beg = $1;
my $end = $2;
if ( $queryHits{$sbjct}->{'or'} eq "Minus" ) {
$beg = $2;
$end = $1;
}
if ( !defined $queryHits{$sbjct}
|| !defined $queryHits{$sbjct}->{'beg'}
|| $queryHits{$sbjct}->{'beg'} > $beg )
{
$queryHits{$sbjct}->{'beg'} = $beg;
}
if ( !defined $queryHits{$sbjct}
|| !defined $queryHits{$sbjct}->{'end'}
|| $queryHits{$sbjct}->{'end'} < $beg )
{
$queryHits{$sbjct}->{'end'} = $end;
}
}
}
# Trailing case
if ( defined $queryHits{'query'} )
{
my ( $class, $orient, $pVal ) =
&chooseBestBlastX(
queryHits => \%queryHits,
pValues => \%pValues,
masklevel => $masklevel
);
$bxResults{ $queryHits{'query'} } = { 'class' => $class,
'orient' => $orient,
'pVal' => $pVal };
}
close BXTP;
return ( \%bxResults );
}
##---------------------------------------------------------------------##
## Use: &chooseBestBlastX( queryHits => $queryHitsRef,
## pValues => \%pValues,
## masklevel => $masklevel );
##
## Returns
##
##---------------------------------------------------------------------##
sub chooseBestBlastX {
my %parameters = @_;
die $CLASS . "::chooseBestBlastX(): Missing queryHits parameter!"
if ( !defined $parameters{'queryHits'} );
die $CLASS . "::chooseBestBlastX(): Missing output parameter!"
if ( !defined $parameters{'masklevel'} );
my $masklevel = $parameters{'masklevel'};
my $queryHits = $parameters{'queryHits'};
my $q = $queryHits->{'query'};
my $oppositestrand = $queryHits->{'oppositestrand'};
my @pastscore = ( 0 );
my @pastend = ( 0 );
my $skip = 0;
my $mostSigPValue = 0;
my @sortedmatches = sort {
die "bega $a $b" unless $queryHits->{$a}->{'beg'};
die "begb $a $b" unless $queryHits->{$b}->{'beg'};
die "scorea $a $b" unless $queryHits->{$a}->{'score'};
die "scoreb $a $b" unless $queryHits->{$b}->{'score'};
( $queryHits->{$a}->{'beg'} <=> $queryHits->{$b}->{'beg'} )
|| ( $queryHits->{$a}->{'score'} <=> $queryHits->{$b}->{'score'} );
} grep { !/query|oppositestrand/ } keys %{$queryHits};
my $nr = 0;
my ( $lastclass, $lastori, $classunknown, $oriunknown );
if ( $#sortedmatches >= 0 ) {
SUBJECTS:
foreach my $subj ( @sortedmatches ) {
my $matchlength =
$queryHits->{$subj}->{'end'} - $queryHits->{$subj}->{'beg'} + 1;
my $minlength =
( $queryHits->{$subj}->{'end'} - $queryHits->{$subj}->{'beg'} + 1 ) *
( 100 - $masklevel ) / 100;
my $i = $nr + 1;
while ( $sortedmatches[ $i ]
&& $queryHits->{ $sortedmatches[ $i ] }->{'beg'} -
$queryHits->{$subj}->{'beg'} < $minlength )
{
if (
$queryHits->{ $sortedmatches[ $i ] }->{'p'} <
$queryHits->{$subj}->{'p'}
|| $queryHits->{ $sortedmatches[ $i ] }->{'p'} ==
$queryHits->{$subj}->{'p'} # i.e. usually: they're both 0.
&& $queryHits->{ $sortedmatches[ $i ] }->{'score'} >
$queryHits->{$subj}->{'score'}
)
{
if ( $queryHits->{$subj}->{'end'} <=
$queryHits->{ $sortedmatches[ $i ] }->{'end'}
|| $queryHits->{ $sortedmatches[ $i ] }->{'beg'} -
$queryHits->{$subj}->{'beg'} + $queryHits->{$subj}->{'end'} -
$queryHits->{ $sortedmatches[ $i ] }->{'end'} < $minlength )
{
++$nr;
next SUBJECTS;
}
}
++$i;
}
$i = $nr - 1;
while ( $i >= 0 ) {
if (
(
$queryHits->{ $sortedmatches[ $i ] }->{'p'} <
$queryHits->{$subj}->{'p'}
|| $queryHits->{ $sortedmatches[ $i ] }->{'p'} ==
$queryHits->{$subj}->{'p'} # i.e. usually: they're both 0.
&& $queryHits->{ $sortedmatches[ $i ] }->{'score'} >
$queryHits->{$subj}->{'score'}
)
&& $queryHits->{$subj}->{'end'} -
$queryHits->{ $sortedmatches[ $i ] }->{'end'} < $minlength
)
{
++$nr;
next SUBJECTS;
}
--$i;
}
# I want to actually compare the matches that come through here
# and discard those that score much lower and are overlapped
# by > 90% by a combination of other matches
if ( $subj =~ /(\S+)\#(\S+)/ ) {
my $name = $1;
my $class = $2;
# Though usually the orientation of the genes define the
# orientation of the transposable element, proteins can be
# encoded on both strands. Proteins on the reverse strand
# are found for example in Gypsy retrotransposons and MuDR
# DNA transposons. They're indicated with the label
# "#ReverseORF" right after the name
print SUMR "$q\t$queryHits->{ $subj }->{ 'beg' } "
. "$queryHits->{ $subj }->{ 'end' }\t$name\t$class\t"
. "$queryHits->{ $subj }->{ 'or' }\t"
. "$queryHits->{ $subj }->{ 'score' }\t"
. "$queryHits->{ $subj }->{ 'identical' }\/"
. "$queryHits->{ $subj }->{ 'aligned' }\t"
. "$queryHits->{ $subj }->{ 'positives' }\/"
. "$queryHits->{ $subj }->{ 'aligned' }\t"
. "$queryHits->{ $subj }->{ 'p' }\n";
$class =~ s/-gene$//;
if ( $lastclass && $class !~ /^$lastclass/ && $lastclass !~ /^$class/ )
{
print " ! Clashing classes: $q $lastclass $class\n"
if ( $DEBUG );
# perhaps if a p value is > 10 orders of magnitude smaller for one
# class than an other, and the protein matches at least partially
# overlap, take the better p value
if ( $class =~ /LTR\/ERV/ && $lastclass =~ /LTR\/ERV/ ) {
# there are some proteins in the database of
# mosaic elements combining the three families
$class = "LTR/ERV";
}
else {
$lastclass =~ s/\/.+//; # deleting backslash and stuff after it
if ( $class =~ /^$lastclass/ ) {
$class = $lastclass;
}
else {
++$classunknown;
}
}
}
if ( $queryHits->{$subj}->{'$oppositestrand'} ) {
$queryHits->{$subj}->{'or'} =~ s/Minus/Plus/
|| $queryHits->{$subj}->{'or'} =~ s/Plus/Minus/;
}
if ( $lastori && $queryHits->{$subj}->{'or'} ne $lastori ) {
print " ! Clashing orientations: $q\n"
if ( $DEBUG );
++$oriunknown;
}
$lastclass = $class;
$lastori = $queryHits->{$subj}->{'or'};
}
else {
print SUMR "$q\t$queryHits->{ $subj }->{ 'beg' } "
. "$queryHits->{ $subj }->{ 'end' }\t$subj\t-\t-"
. "$queryHits->{ $subj }->{ 'or' }\t"
. "$queryHits->{ $subj }->{ 'score' }\t"
. "$queryHits->{ $subj }->{ 'identical' }\/"
. "$queryHits->{ $subj }->{ 'aligned' }\t"
. "$queryHits->{ $subj }->{ 'positives' }\/"
. "$queryHits->{ $subj }->{ 'aligned' }\t"
. "$queryHits->{ $subj }->{ 'p' }\n";
}
$mostSigPValue = $queryHits->{$subj}->{'p'}
if ( $mostSigPValue == 0
|| $queryHits->{$subj}->{'p'} < $mostSigPValue );
#print "Most sig pVal = $mostSigPValue, lastclass = $lastclass\n" if ( $DEBUG );
++$nr;
}
$lastclass = "Unknown" if $classunknown;
$lastori = "" if ( $oriunknown );
print "ChooseBestBlastX::Returning( $lastclass, $lastori, $mostSigPValue )\n" if ( $DEBUG );
return( $lastclass, $lastori, $mostSigPValue );
}
else {
print "ChooseBestBlastX::Returning( Unknown )\n" if ( $DEBUG );
return( "Unknown", "", "" );
}
}
##---------------------------------------------------------------------##
## Use: &vsRMLibAnalysis( searchResults => $resultsRef,
## pValues => \%pValues );
##
## Returns
##
##---------------------------------------------------------------------##
sub vsRMlibAnalysis {
my %parameters = @_;
die $CLASS . "::vsRMlibAnalysis(): Missing searchResults parameter!"
if ( !defined $parameters{'searchResults'} );
my $resultCol = $parameters{'searchResults'};
die $CLASS . "::vsRMlibAnalysis(): Missing blastXResults parameter!"
if ( !defined $parameters{'blastXResults'} );
my ( %class, %ori ) = ();
my $blastXResults = $parameters{'blastXResults'};
# note that this sub is reading in a modified cross_match file
# similar to the repeatmasker .out file having "+" for forward strand matches
# so that all lines have the same number of columns.
# They do not have the query and subject names split on #
my ( %combscore, $oriented, @dnaclass, @ori );
my $query;
my $origquery;
my $protclass;
# Initialize ds with bx results
foreach my $bxResultsKey ( keys( %{ $blastXResults } ) )
{
$class{ $bxResultsKey } = $blastXResults->{ $bxResultsKey }->{'class'};
$ori{ $bxResultsKey } = $blastXResults->{ $bxResultsKey }->{'orient'};
}
for ( my $i = 0 ; $i < $resultCol->size() ; $i++ ) {
my $result = $resultCol->get( $i );
#print "RESULT:" . $result->toStringFormatted() . "\n" if ( $DEBUG );
#print "RESULT:" . $result->toStringFormatted() . "\n";
#print "RESULT: $query\n";
if ( $query && $result->getQueryName() ne $query ) {