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ProcessRepeats
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ProcessRepeats
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#!/usr/bin/perl
##---------------------------------------------------------------------------##
## File:
## @(#) ProcessRepeats
## Authors:
## Arian Smit <[email protected]>
## Robert Hubley <[email protected]>
## Description:
## Takes RepeatMasker output and produces an annotation table.
##
##
#******************************************************************************
#*
#* Copyright (C) Institute for Systems Biology 2002-2012 Developed by
#* Arian Smit and Robert Hubley.
#*
#* Copyright (C) Arian Smit 2000-2001
#*
#* Copyright (C) University of Washington 1996-1999 Developed by Arian Smit,
#* Philip Green and Colin Wilson of the University of Washington Department of
#* Genomics.
#*
#* 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
#
# $Log$
#
###############################################################################
#
#
=head1 NAME
ProcessRepeats - Post process results from RepeatMasker and produce an annotation file.
=head1 SYNOPSIS
ProcessRepeats [-options] <RepeatMasker *.cat file>
=head1 DESCRIPTION
The options are:
=over 4
=item -h(elp)
Detailed help
=item -species <query species>
Post process RepeatMasker results run on sequence from
this species. Default is human.
=item -lib <libfile>
Skips most processing, does not produce a .tbl file unless
the custome library is in the ">name#class" format.
=item -nolow
Does not display simple repeats or low_complexity DNA in the annotation.
=item -noint
Skips steps specific to interspersed repeats, saving lots of time.
=item -lcambig
Outputs ambiguous DNA transposon fragments using a lower case
name. All other repeats are listed in upper case. Ambiguous
fragments match multiple repeat elements and can only be
called based on flanking repeat information.
=item -u
Creates an untouched annotation file besides the manipulated file.
=item -xm
Creates an additional output file in cross_match format (for parsing).
=item -ace
Creates an additional output file in ACeDB format.
=item -gff
Creates an additional Gene Feature Finding format.
=item -poly
Creates an output file listing only potentially polymorphic simple repeats.
=item -no_id
Leaves out final column with unique number for each element (was default).
=item -excln
Calculates repeat densities excluding long stretches of Ns in the query.
=item -orf2
Results in sometimes negative coordinates for L1 elements; all L1 subfamilies
are aligned over the ORF2 region, sometimes improving interpretation of data.
=item -a
Shows the alignments in a .align output file.
=item -maskSource <originalSeqenceFile>
Instructs ProcessRepeats to mask the sequence file using the annotation.
=item -x
Mask repeats with a lower case 'x'.
=item -xsmall
Mask repeats by making the sequence lowercase.
=back
=head1 SEE ALSO
=over 4
RepeatMasker, Crossmatch, Blast
=back
=head1 COPYRIGHT
Copyright 2002-2012 Arian Smit, Robert Hubley, Institute for Systems Biology
=head1 AUTHORS
Arian Smit <[email protected]>
Robert Hubley <[email protected]>
=cut
#
# Module Dependence
#
use strict;
use FindBin;
use lib $FindBin::RealBin;
use SeqDBI;
use FileHandle;
use FastaDB;
use SearchResult;
use SearchEngineI;
use SearchResultCollection;
use ArrayList;
use CrossmatchSearchEngine;
use Getopt::Long;
use Taxonomy;
use Data::Dumper;
use PRSearchResult;
use Matrix;
use RepeatMaskerConfig;
# This is a special database-specific module
my $LIBDIR;
BEGIN {
my $config = $RepeatMaskerConfig::configuration;
$LIBDIR = $config->{'LIBDIR'}->{'value'};
}
use lib $LIBDIR;
use RepeatAnnotationData;
# Global variables
my $DEBUG = 0;
#
# Refinement Hash:
# Contains re-alignments for *.cat alignments which were refined.
# structure is as follows:
# $refinementHash{ "b#s#i#" }->{ ConsensusID } = ( annot1ref, annot2ref, ...)
#
my %refinementHash = (); # Contains refined annotations ordered by catID
my %chainSeq1Length;
# A bug in 5.8 produces way too many warnings
if ( $] && $] >= 5.008003 ) {
use warnings;
}
#
# Option processing
# e.g.
# -t: Single letter binary option
# -t=s: String parameters
# -t=i: Number paramters
#
my @opts =
qw (a ace debug excln gff lib=s noint nolow orf2 orifile=s no_id poly species=s u xm mammal mus rat rod|rodent cow pig artiodactyl cat dog carnivore chicken fugu danio drosophila elegans arabidopsis rice wheat maize primate maskSource=s xsmall x lcambig source html );
#
# Get the supplied command line options, and set flags
#
my %options = ();
unless ( &GetOptions( \%options, @opts ) ) {
exec "pod2text $0";
exit( 0 );
}
## Print the internal POD documentation if something is missing
if ( $#ARGV == -1 && !$options{'help'} ) {
print "No cat 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;
}
##
## option -source is now a deprecated option. We only save
## the source alignments if -a is used
##
if ( $options{'a'} ) {
$options{'source'} = 1;
}
else {
$options{'source'} = 0;
}
##
## Species Options and Taxonomy Processing
##
## NOTE: Tax needs to be global for the moment
my $tax;
if ( $options{'species'} ) {
# Need to set opt_species, opt_mammal, opt_mus
$tax =
Taxonomy->new( famdb_dir => "$LIBDIR/famdb" );
if ( $tax->isA( $options{'species'}, "primates" ) ) {
$options{'primate'} = 1;
}
elsif ( $tax->isA( $options{'species'}, "rodentia" ) ) {
$options{'mus'} = 1;
}
elsif ( $tax->isA( $options{'species'}, "mammalia" ) ) {
$options{'mammal'} = 1;
}
}
else {
if ( ! $options{'lib'} ) {
$options{'species'} = "homo";
$options{'primate'} = 1;
}
}
# warning for debug mode
print "Note that in debug mode the IDs are not adjusted to go up stepwise\n\n"
if $options{'debug'};
#
# Check library type used
#
# TODO: We need different levels of meta data compliance. Ie.
# Pound formatting isn't enough anymore. Also we can glean
# compliance like pound formatting from the cat file. No
# need to open up the lib ( yet ).
my $poundformat = "";
if ( $options{'lib'} ) {
open( IN, $options{'lib'} );
while ( <IN> ) {
if ( /^>\S+\#\S+/ ) {
$poundformat = 1;
# Assuming that this represents my classification formatting; no sure
# thing could make it more restrictive by also requiring a backslash
last;
}
}
}
else {
$poundformat = 1;
}
#
# Loop over input files
#
foreach my $file ( @ARGV ) {
if ( $file =~ /.*\.gz$/ ) {
open( INCAT, "gunzip -c $file |" ) || die "Can\'t open file $file\n";
}
else {
open( INCAT, $file ) || die "Can\'t open file $file\n";
}
# INITIALIZE CAT FILE DATA
# Read the cat file and calculate:
# - The length of the original sequence ( minus 1/2 of the overlap )
# - The number of N bases
# - The number of sequences
# - The length of each sequence
# - The fraction GC the version the masked length and the dbversion.
# Also...grab batch overlap boundaries if information is present.
my %batchOverlapBoundaries = ();
my $numSearchedSeqs = 0;
my $lenSearchedSeqs = 0;
my $lenSearchedSeqsExcludingXNRuns = 0;
my $lenSearchedSeqsExcludingAmbig = 0;
my $versionmode = "";
my $engine = "";
my $dbversion = "";
while ( <INCAT> ) {
if ( /^##\s*(\S+)\s+([\d\s,]+)/ ) {
$batchOverlapBoundaries{$1} = [ sort( split( /,/, $2 ) ) ];
}
elsif ( /^##\s*Total\s+Sequences:\s*(\d+)/i ) {
$numSearchedSeqs = $1;
}
elsif ( /^##\s*Total\s+Length:\s*(\d+)/i ) {
$lenSearchedSeqs = $1;
}
elsif ( /^##\s*Total\s+NonMask.*:\s*(\d+)/i ) {
$lenSearchedSeqsExcludingXNRuns = $1;
}
elsif ( /^##\s*Total\s+NonSub.*:\s*(\d+)/i ) {
$lenSearchedSeqsExcludingAmbig = $1;
}
elsif ( /^RepeatMasker|run|RepBase|RM/ ) {
my @bit = split;
$versionmode = $_ if $bit[ 0 ] eq 'RepeatMasker';
$engine = $1 if /^(run with.*)/;
# Since 4.1.1 we are now using famdb. The version is reported a bit
# differently.
# RM Library: CONS-Dfam_withRBRM_3.3
#
if ( /^(RepBase.*)/ || /^RM Library:\s+(\S.*)/ ) {
$dbversion = $1;
last;
}
}
}
close INCAT;
#
# Parse the cat file into an object
#
my $sortedAnnotationsList = undef;
# Always read in alignment data
$sortedAnnotationsList = &parseCATFile( file => $file );
#
# Separate out refined annotations
#
my $annotIter = $sortedAnnotationsList->getIterator();
while ( $annotIter->hasNext() ) {
my $currentAnnot = $annotIter->next();
if ( $currentAnnot->getClassName() eq "" ) {
$currentAnnot->setClassName( "Unspecified" );
}
if ( $currentAnnot->getLineageId() =~ /\[/ ) {
$annotIter->remove();
$currentAnnot->setOrientation( "+" )
if ( $currentAnnot->getOrientation() ne "C" );
my $catID = $currentAnnot->getLineageId();
die "Missing cat file ID for refined element!"
. Dumper( $currentAnnot ) . "\n"
if ( $catID eq "" );
$catID =~ s/[\[\]]//g;
push @{ $refinementHash{$catID}->{ $currentAnnot->getHitName() } },
( $currentAnnot );
}
}
# Create some filename constants
my $catfile = $file;
$file =~ s/\.(temp)?cat(.gz)?$//;
my $filename = $file;
$filename =~ s/(.*\/)//;
unless ( $sortedAnnotationsList->size() > 0 ) {
my $filenaam = $file;
$filenaam = $options{'orifile'} if $options{'orifile'};
open( OUT, ">$file.out" );
print "\n\n\nNo repetitive sequences were detected in $filenaam\n";
print OUT "There were no repetitive sequences detected in $filenaam\n";
close( OUT );
next;
}
print "processing output: ";
open( OUTRAW, ">$file.ori.out" ) if ( $options{'u'} || !$poundformat );
#
# Initialize data structures and ID each annotation
#
# Makes global %seq1Lengths
# NOTE: Only needed because we are not updating LeftOver
# when we modify Seq1Beg/End
#
$sortedAnnotationsList->sort( \&byNameBeginEndrevSWrev );
my $cycleAnnotIter = $sortedAnnotationsList->getIterator();
my %seq1Lengths = ();
my $i = -1;
while ( $cycleAnnotIter->hasNext() ) {
$i++;
my $currentAnnot = $cycleAnnotIter->next();
$currentAnnot->setPRID( $i );
$currentAnnot->setOrientation( "+" )
if ( $currentAnnot->getOrientation() ne "C" );
# Do this early so we capture all information before it is changed.
# NOTE: I may make derived elements links to the cat file for
# memory brevity.
if ( $options{'source'} ) {
$currentAnnot->addDerivedFromAnnot( $currentAnnot );
$currentAnnot->setAlignData( undef );
}
my $HitName = $currentAnnot->getHitName();
$HitName =~ s/_short_$//;
# RMH 11/21/12: Added for Dfam
$HitName =~ s/_offset$//;
$currentAnnot->setHitName( $HitName );
if ( !defined $seq1Lengths{ $currentAnnot->getQueryName() }
|| $seq1Lengths{ $currentAnnot->getQueryName() } <
( $currentAnnot->getQueryEnd() + $currentAnnot->getQueryRemaining() ) )
{
$seq1Lengths{ $currentAnnot->getQueryName() } =
$currentAnnot->getQueryEnd() + $currentAnnot->getQueryRemaining();
}
}
print "\ncycle 1 ";
#printHitArrayList( $sortedAnnotationsList );
my ( $chainBegRef, $chainEndRef ) = &cycleReJoin( $sortedAnnotationsList );
my %chainBeg = %{$chainBegRef};
my %chainEnd = %{$chainEndRef};
########################## C Y C L E 2 ###############################
# Purpose: Remove Edge Effect Annotations
# Remove Masklevel violations
# Rename Satellite Shifted Copies
# build DNA transposon equivalency datastructure
##########################################################################
print "\ncycle 2 ";
# Sort by name, begin position, and end position descending
$sortedAnnotationsList->sort( \&byNameBeginEndrevSWrev );
# Create an ArrayListIterator for this cycle
$cycleAnnotIter = $sortedAnnotationsList->getIterator();
my %colWidths = &getMaxColWidths( $sortedAnnotationsList );
my $DEBUG = 0;
$i = -1;
CYCLE2:
while ( $cycleAnnotIter->hasNext() ) {
$i++;
print "." if ( $i + 1 ) % 1000 == 0;
# NOTE: An iterator's index is considered
# to be in between elements of a datastructure.
# To obtain the correct index for the
# current element in this pass we should
# get the index *before* we move the iterator.
my $currentIndex = $cycleAnnotIter->getIndex();
my $currentAnnot = $cycleAnnotIter->next();
if ( $DEBUG ) {
print "CYCLE2: Considering\n";
$currentAnnot->print();
}
# TODO: This recursion violation code might not be necessary
# once the cycleReJoin code is changed to use the new *.cat ID field
# or not: What if RM fragmented two overlapping alignments:
# maskelevel 90:
# ------^-------->
# ----------^----->
# You would have
# ++++++++++
# -----/ \--------->
# ++++++++++
# and ----------------/ \----->
#
# HMMM...have to think about this. This is a fine dance with the
# search engine maskelevel parameter.
#
if ( $currentAnnot->getRightLinkedHit() ) {
my $proxIter = $cycleAnnotIter->getIterator();
while ( $proxIter->hasNext() ) {
my $nextAnnot = $proxIter->next();
# Quit once we reach our partner
last if ( $nextAnnot == $currentAnnot->getRightLinkedHit() );
# Break Recursion Violations
if ( $currentAnnot->containsElement( $nextAnnot )
&& $nextAnnot->containsElement( $currentAnnot->getRightLinkedHit() ) )
{
if ( $DEBUG ) {
print "This violates recursion:\nFirst:\n";
$currentAnnot->printLeftRightLinks();
print "Second:\n";
$nextAnnot->printLeftRightLinks();
}
# Break lower scoring link
my $oldRight = $nextAnnot->getRightLinkedHit();
$nextAnnot->setRightLinkedHit( undef );
$oldRight->setLeftLinkedHit( undef );
}
}
}
##
## Edge Effect Removal
##
## The current method of processing overlaps, while better
## than before still produces some edge effects. This
## section attempts to remove these before we start any
## serious analysis.
##
## Overlaps are handled in RepeatMasker thus:
##
## Middle
## <------ |
## ----->
## Batch#1 | ----x---->
## ...-----------------------------|
## |
## |
## |-----------------------------...
## | BATCH#2
## <-x- |
## ---->
## | ---------------->
##
##
## RepeatMasker deletes all annotations which are
## contained in the region left/right ( closest to
## the edge ) of the overlap midpoint. Shown here
## with an "x" in the diagram annotations.
## If an annotation spans the midpoint it is kept
## in the cat file. This leaves several types of
## edge effects in annoation:
##
## Perfect or Near Perfect duplicates. Perfect if
## the same matrix was used and the annotation is
## completely contained in the overlap. Near perfect
## otherwise.
##
## Middle
## |
## ----->
## |
## ----->
##
##
## Cut Level Ambiguities. A full length young repeat
## partially contained in the overlap will be excised
## at a lower cutlevel in one batch and masked at
## a higher cutlevel in the other batch. See below
## for some examples.
##
##
# Remove exact duplicates. Near duplicates get resolved elsewhere
# ( FuseOverlappingSeqs etc ). We do this now especially to handle
# duplicated poly-a tails that we are about to join.
my $prevAnnot = $sortedAnnotationsList->get( $currentIndex - 1 )
if ( $currentIndex > 0 );
if ( $prevAnnot
&& $currentAnnot->getScore() == $prevAnnot->getScore()
&& $currentAnnot->getPctDiverge() == $prevAnnot->getPctDiverge()
&& $currentAnnot->getQueryName() eq $prevAnnot->getQueryName()
&& $currentAnnot->getQueryStart() == $prevAnnot->getQueryStart()
&& $currentAnnot->getQueryEnd() == $prevAnnot->getQueryEnd() )
{
# Lower Scoring Overlap > %90 Covered by Higher Scoring
# Get rid of lower scoring one
# same cutlevel
if ( $DEBUG ) {
print "REMOVING EXACT DUPLICATE:\n";
$currentAnnot->print();
print " because of:\n";
$prevAnnot->print();
}
#$prevAnnot->addDerivedFromAnnot( $currentAnnot )
# if ( $options{'source'} );
# Fix any previous joins to this element
$currentAnnot->removeFromJoins();
$cycleAnnotIter->remove();
next CYCLE2;
}
#
# If a large >1000bp ( 1/2 current overlap distance )
# young repeat starts outside the overlap and spans
# the middle of the overlap you will get edge effect
# duplications. I.e.
#
# Case #1 Middle
# batch1 |
# ---------------------------|
# -----------------> ( excised cutlevels 0-4 )
# ----X----> ( masked cutlevel 5 )
# |------------------------------
# | batch2
# |
# or |
# batch1 ----X--> ( masked cutlevel 5 )
# ----------------------------|
# |------------------------------- batch2
# -----------------> ( excised cutlevel 0-4 )
# |
#
# Because excision is only performed on full length
# elements (lines can be 5' truncated) this can be
# detected by checking for elements which are contained by
# a masked annotation *and* are cut out.
#
# Case #2 Middle
# |
# <---X--- (masked..just outside the other )
# ----------------------------|
# |-------------------------------
# | <---------- (cut)
# |
# |
# Case #3 |
# (masked) --> |
# -------> (cut)
# -----------------------------|
# |----------------------------
# X> |
# -------->
#
# In this case you have a cut out element spaning a middle
# which is one bp longer in one batch. This creates
# a 1bp overlap with a something which has been masked.
#
# So our general rule ends up: Remove all masked elements
# which overlap ( by > 10bp ) or are contained by another
# cut out element.
# These cases should never occur outside the overlap
# region anyway.
#
if ( $currentAnnot->isMasked() ) {
my $proxIter = $cycleAnnotIter->getIterator();
$proxIter->previous();
while ( $proxIter->hasPrevious() ) {
my $prevAnnot = $proxIter->previous();
last
unless ( $currentAnnot->getQueryName eq $prevAnnot->getQueryName()
&& $prevAnnot->getQueryEnd() >= $currentAnnot->getQueryStart() );
if ( $prevAnnot->isCut()
&& $prevAnnot->getQueryEnd() - $currentAnnot->getQueryStart() >= 10 )
{
if ( $DEBUG ) {
print "DELETING MASKED INSIDE CUT:\n";
$currentAnnot->print();
print " because of previous:\n";
$prevAnnot->print();
}
# Fix any previous joins to this element
$currentAnnot->removeFromJoins();
$cycleAnnotIter->remove();
next CYCLE2;
}
}
$proxIter = $cycleAnnotIter->getIterator();
while ( $proxIter->hasNext() ) {
my $nextAnnot = $proxIter->next();
last
unless ( $currentAnnot->getQueryName eq $nextAnnot->getQueryName()
&& $nextAnnot->getQueryStart() <= $currentAnnot->getQueryEnd() );
if ( $nextAnnot->isCut()
&& $currentAnnot->getQueryEnd() - $nextAnnot->getQueryStart() >= 10 )
{
if ( $DEBUG ) {
print "DELETING MASKED INSIDE CUT:\n";
$currentAnnot->print();
print " because of next:\n";
$nextAnnot->print();
}
#$nextAnnot->addDerivedFromAnnot( $currentAnnot )
# if ( $options{'source'} );
# Fix any previous joins to this element
$currentAnnot->removeFromJoins();
$cycleAnnotIter->remove();
next CYCLE2;
}
}
}
#
# Masklevel Violations From Clipping Boundaries
#
# RepeatMasker fragments alignments which span
# cut out elements. This fragmentation process may
# convert a pair of alignments like:
#
# --------------^-------------> SW=1000
# -----------^-----------------> SW=1500
#
# ( where "^" marks the site of a clipped out element )
# into something like:
#
# SW = 1000 SW = 1000
# --------------> ------------->
# -----------> ----------------->
# SW = 1500 SW = 1500
#
# This little block of code resolves this masklevel
# rule-breaker ( lower scoring alignment contained by
# higher scoring one ) by elminating the lower scoring
# subfragments.
#
# i.e Delete element if flanking elements include
# it and has a better or equal score.
#
# SW = 1000
# -------------->
# -----------> ----------------->
# SW = 1500 SW = 1500
#
# This is still a bit artificial.
#
$prevAnnot = $sortedAnnotationsList->get( $currentIndex - 1 )
if ( $currentIndex > 0 );
my $proxIter = $cycleAnnotIter->getIterator();
my ( $prevHitName, $prevClassName ) =
split( /\#/, $prevAnnot->getSubjName() )
if ( $prevAnnot );
#
# Delete iff:
# ----current-----^ SW <= past
# -----past-------^
# -..----past----------^
#
# or
# ^---current----- SW <= past
# ^----past-------
# ^------past----------...--
#
if (
$prevAnnot
&& (
(
$currentAnnot->getQueryEnd() == $prevAnnot->getQueryEnd()
&& $currentAnnot->getScore() <= $prevAnnot->getScore()
&& $currentAnnot->getQueryName() eq $prevAnnot->getQueryName()
&& $currentAnnot->getClassName() eq $prevClassName
)
|| ( $currentAnnot->getQueryStart() == $prevAnnot->getQueryStart()
&& $currentAnnot->getQueryEnd() <= $prevAnnot->getQueryEnd()
&& $currentAnnot->getScore() <= $prevAnnot->getScore()
&& $currentAnnot->getQueryName() eq $prevAnnot->getQueryName()
&& $currentAnnot->getClassName() eq $prevClassName )
)
)
{
if ( $DEBUG ) {
print "Deleting clipping boundary fragment "
. "( masklevel violation ):\n";
$prevAnnot->print();
$currentAnnot->print();
}
#$prevAnnot->addDerivedFromAnnot( $currentAnnot )
# if ( $options{'source'} );
# Fix any previous joins to this element
$currentAnnot->removeFromJoins();
$cycleAnnotIter->remove();
next CYCLE2;
}
my $Seq2BeginPrint = $currentAnnot->getSubjStart();
my $LeftUnalignedPrint = "(" . $currentAnnot->getSubjRemaining() . ")";
my $LeftOverPrint = "(" . $currentAnnot->getQueryRemaining() . ")";
if ( $currentAnnot->getOrientation() eq "C" ) {
$Seq2BeginPrint = "(" . $currentAnnot->getSubjRemaining() . ")";
$LeftUnalignedPrint = $currentAnnot->getSubjStart();
}
#
# Supposedly creates an untouched annotation file.
# What it really does is create an annotation file
# which has been modified to remove exact duplicates
# and batch overlap artifacts only.
#
if ( $options{'u'} || !$poundformat ) {
my $prevAnnot = $sortedAnnotationsList->get( $currentIndex - 1 )
if ( $currentIndex > 0 );
my $nextAnnot = $sortedAnnotationsList->get( $currentIndex + 1 )
if ( $currentIndex < $sortedAnnotationsList->size() - 1 );
my $Overlapped = "";
if ( $prevAnnot
&& $currentAnnot->getQueryStart() <= $prevAnnot->getQueryEnd()
&& $currentAnnot->getScore() < $prevAnnot->getScore()
|| $nextAnnot
&& $currentAnnot->getQueryEnd() >= $nextAnnot->getQueryStart()
&& $currentAnnot->getScore() < $nextAnnot->getScore() )
{
$Overlapped = "*";
}
$currentAnnot->setClassName( "" )
unless ( $currentAnnot->getClassName() );
#
# sequence names get truncated to 20 letters. Too
# cumbersome to change. However, names like
# /mnt/user/users/FlipvanTiel/mystuff/sequence1 better be
# clipped from the end. Thus:
$currentAnnot->setQueryName(
substr( $currentAnnot->getQueryName(), -20 ) )
if ( length $currentAnnot->getQueryName() > 20
&& $currentAnnot->getQueryName() =~ /^\// );
printf OUTRAW "%6d %4s %4s %4s %20s %9s %9s %8s %1s "
. "%20s %15s %7s %7s %7s %3s\n", $currentAnnot->getScore(),
$currentAnnot->getPctDiverge, $currentAnnot->getPctDelete,
$currentAnnot->getPctInsert, $currentAnnot->getQueryName(),
$currentAnnot->getQueryStart(), $currentAnnot->getQueryEnd(),
"(" . $currentAnnot->getQueryRemaining() . ")",
$currentAnnot->getOrientation(), $currentAnnot->getHitName(),
$currentAnnot->getClassName(), $Seq2BeginPrint,
$currentAnnot->getSubjEnd(), $LeftUnalignedPrint;
$Overlapped;
} # if ( $options{'u'} || !$poundformat )
#
# If a user supplied non-classified library was used
#
if ( !$poundformat ) {
if ( $options{'ace'} ) {
if ( $currentAnnot->getOrientation() eq "C" ) {
print OUTACE "Motif_homol \""
. $currentAnnot->getHitName()
. "\" \"RepeatMasker\" "
. $currentAnnot->getPctDiverge() . " "
. $currentAnnot->getQueryStart() . " "
. $currentAnnot->getQueryEnd() . " - "
. $currentAnnot->getSubjEnd() . " "
. $currentAnnot->getSubjStart() . "\n";
}
else {
print OUTACE "Motif_homol \""
. $currentAnnot->getHitName()
. "\" \"RepeatMasker\" "
. $currentAnnot->getPctDiverge() . " "
. $currentAnnot->getQueryStart() . " "
. $currentAnnot->getQueryEnd() . " + "
. $currentAnnot->getSubjStart() . " "
. $currentAnnot->getSubjEnd() . "\n";
}
}
if ( $options{'xm'} ) {
my $tempclassname = "";
$tempclassname = "\#" . $currentAnnot->getClassName()
if ( $currentAnnot->getClassName() );
print OUTXM $currentAnnot->getScore() . " "
. $currentAnnot->getPctDiverge() . " "
. $currentAnnot->getPctDelete() . " "
. $currentAnnot->getPctInsert() . " "
. $currentAnnot->getQueryName() . " "
. $currentAnnot->getQueryStart() . " "
. $currentAnnot->getQueryEnd() . " "
. $LeftOverPrint . " "
. $currentAnnot->getOrientation() . " "
. $currentAnnot->getHitName()
. $tempclassname . " "
. $Seq2BeginPrint . " "
. $currentAnnot->getSubjEnd() . " "
. $LeftUnalignedPrint . "\n";
}
if ( $options{'gff'} ) {
#my $source;
#if ( $currentAnnot->getHitName() =~ /Alu/ ) {
# $source = 'RepeatMasker_SINE';
#}
#else { #
# $source = 'RepeatMasker';
#}
my $source = 'RepeatMasker';
print OUTGFF ""
. $currentAnnot->getQueryName()
. "\t$source\tdispersed_repeat\t"
. $currentAnnot->getQueryStart() . "\t"
. $currentAnnot->getQueryEnd() . "\t"
. $currentAnnot->getPctDiverge() . "\t"
. ( $currentAnnot->getOrientation() eq 'C' ? '-' : '+' ) . "\t.\t"
. "ID=" . $currentAnnot->getPRID()+1 . ";"
. "Target \"Motif:"
. $currentAnnot->getHitName() . "\" "
. $currentAnnot->getSubjStart() . " "
. $currentAnnot->getSubjEnd() . "\n";
}
} # if ( !$poundformat )
else {
#
# Satellite Consensi
# Searching for satellites with consensi is a hack.
# Search engines such as crossmatch will often return
# hits to a single repeating pattern as:
# | | | | |
# abcdefghabcdefghabcdefghabcdefghabcdefgh
# --------->
# -------->
# -------->
# By creating a consensus for the repeat pattern and
# another for the same pattern shifted by 1/2 of the
# cycle. You can nicely overlapping hits.
# These shifted consensi are denoted by the use of a
# trailing "_" in the name.
#
# Here is the regular expression for the syntax:
#
# [A-Z_]+[a-z]?_?#Satellite
#
# So here are some examples:
#
# ALR_#Satellite
# ALRa#Satellite
# ALRa_#Satellite
# CENSAT_MC#Satellite
#
# Since these trailing "_" variants and the "[a-z]"
# variants are equivalent we only need to restore
# the original name by stripping these characters
# HitName.
#
# NOTE: The lowercase varieties are not in repbase.
#
if ( $currentAnnot->getClassName =~ /Satellite/ ) {
my $HitName = $currentAnnot->getHitName();
$HitName =~ s/_(offset)?$//;
# This was truncating newer statellite names which use the
# _??? to indicate species names.
if ( $HitName =~ /ALR|BSR/ && $HitName !~ /_/ ) {
$HitName =~ s/[a-z]$//;
}
$currentAnnot->setHitName( $HitName );
}
if ( $currentAnnot->getClassName =~ /DNA/ ) {
# Find all ambiguous dna transposon fragments and generate
# equivalency lists
&preProcessDNATransp( \%chainBeg, \%chainEnd, $currentAnnot,
\%RepeatAnnotationData::repeatDB );
}
}
} # END CYCLE 2
close( OUTRAW ) if ( $options{'u'} || !$poundformat );
#
# If we do not have a pound formatted database we are done!
#
if ( !$poundformat ) {
&generateOutput(
\%options, \%seq1Lengths,
$file, $filename,
$dbversion, $numSearchedSeqs,
$lenSearchedSeqs, $lenSearchedSeqsExcludingXNRuns,