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#!/usr/bin/perl
use strict;
use warnings;
my $offset=0;
my @output;
if (@ARGV) {
$offset = shift @ARGV;
}
my $target;
my ($from, $to) = ($offset, $offset+10000);
my $name="AUGUSTUS";
while (<>) {
chomp;
my $comment = "";
if (/^# .* --predictionStart=(\d+) --predictionEnd=(\d+)/) {
($from, $to) = ($1 + $offset -1000, $2 + $offset +1000);
$from = 0 if $from < 0;
}
if (/^# .* --proteinprofile/) {
$name .= "-PPX";
}
$comment = $1 if s/\s*\#.*$//;
my @line = split /\t/;
next unless @line == 9;
next if $line[2] eq "interblock_region";
if ($line[8] =~ /ID=([^;]*)/) {
$line[8]=$1;
} else {
next;
}
$target = $line[0] unless defined $target;
push @output,join("\t", @line)."\n";
}
print "browser position $target:$from-$to hide all\n";
print "track offset=$offset name=\"$name\" description=\"$name prediction\" visibility=3\n";
print foreach @output;
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