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#!/usr/bin/perl
#
# This takes the AUGUSTUS output in the standard input
# and outputs to standard output a file with UCSC browser gtf format
# The display includes tracks for those types of hints that are present in the file.
# Mario 01.08.2006
#
use strict;
my @augustus = <STDIN>;
my $firstseqname="";
my $firstseqbegin=-1;
my $lastseqend=-1;
my ($seqname, $begin, $end, $type, $prgname);
#
# determine the browser position entry
# display the first sequence in the full range of annotation
#
my %hints = ('ass' => 0, 'dss' => 0, 'tss' => 0, 'start' => 0, 'stop' => 0, 'tts' => 0, 'intronpart' => 0, 'intron' => 0,
'UTRpart' => 0, 'CDSpart' => 0, 'nonexonpart' => 0, 'irpart' => 0, 'CDS' => 0, 'UTR' => 0, 'exon' => 0, 'exonpart' => 0);
foreach my $line (@augustus) {
if ($line !~/^#/) {
# expand shortcuts for exonpart, intronpart, CDSpart, ..
$line =~ s/\tep\t/\texonpart\t/;
$line =~ s/\tip\t/\tintronpart\t/;
$line =~ s/\tcp\t/\tCDSpart\t/;
$line =~ s/\tup\t/\tUTRpart\t/;
$line =~ s/\tnep\t/\tnonexonpart\t/;
if ($line =~ /^(\S+)\t(\S+)\t(\S+)\t(\S+)\t(\S+)\t/) {
$seqname = $1;
$prgname = $2;
$type = $3;
$begin = $4;
$end = $5;
if (exists $hints{$type} && !($prgname =~ /^AUGUSTUS/)) {
$hints{$type} += 1;
}
if ($firstseqname eq "") {
$firstseqname = $seqname;
}
if ($seqname eq $firstseqname) {
if ($firstseqbegin < 0 || $lastseqend < 0) {
$firstseqbegin = $begin;
$lastseqend = $end;
}
if ($begin < $firstseqbegin) {
$firstseqbegin = $begin;
}
if ($end > $lastseqend) {
$lastseqend = $end;
}
}
}
}
}
my $browserbegin = $firstseqbegin - 1000;
my $browserend = $lastseqend + 1000;
if ($browserbegin < 1) {
$browserbegin = 1;
}
#print "browser position $firstseqname:$browserbegin-$browserend\n";
my $grpNameCount = 1;
my $grpName;
foreach my $feature (keys %hints) {
next unless $hints{$feature}>0;
print "track name=\"$feature\" description=\"$feature hints\" visibility=3\n";
foreach my $line (@augustus) {
if ($line !~/^#/) {
if ($line =~ /\t$feature\t/ && !($line =~/\tAUGUSTUS/)) {
$line =~ s/;?source=[^;]*;?//;
$line =~ s/;?src=[^;]*;?//;
$line =~ s/grp=//;
$line =~ s/pri=\d+;?//;
$line =~ s/priority=\d+//;
$line =~ s/\t([^\t]*)$//;
$grpName = $1;
$grpName =~ s/\s*\n//;
if ($grpName eq "" || ($grpName =~ /mult=\d+;/)){ # no name, use counter as name so the browser does not complain about same group different strand
$grpName = "" . ($grpNameCount++) . "$grpName";
}
print $line, "\t" , $grpName, "\n";
}
}
}
}
my $haveAUG=0;
foreach my $line (@augustus) {
# $line =~ /\tAUGUSTUS(\d+)\t/;
# if ($1 ne $id) {
# $id = $1;
# print "track name=AUGUSTUS$id description=\"AUGUSTUS $id\" visibility=3\n";
# }
if ($line =~ /\tAUGUSTUS\S*\texon\t/ || $line =~ /\tAUGUSTUS\S*\tCDS\t/) {
print "track name=AUGUSTUS description=\"AUGUSTUS\" visibility=3\n" if (!$haveAUG);
print $line;
$haveAUG = 1;
}
}
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