#!/usr/bin/perl

# Time-stamp: <2005-12-30 14:09:41 kasper>

use warnings;
use strict;
use Getopt::Long;
use constant USAGE =><<END;

SYNOPSIS:

 gffmapback.pl [OPTIONS] [infile [outfile]]

DESCRIPTION:

This script converts GFF lines with first entry in the format:
<ID>-OFFSET:<OFFSET> into just <ID> and adjusts the start and end
coordinates according to <OFFSET>.

OPTIONS:

       --help
             Prints this help.

EXAMPLES:

 gffmapback.pl infile.gff outfile.gff

 cat *.gff | gffbackmap.pl > outfile.gff

DEPENDENCIES:

 None.

AUTHOR:

Kasper Munch

COPYRIGHT:

This program is free software. You may copy, modify, and redistribute
it under the same terms as Perl itself.

END

my $help = 0;

GetOptions(
           "help" => \$help,
          ) or die USAGE;

$help and die USAGE;

@ARGV = ('-') unless @ARGV;
my $input = shift @ARGV;
open my $in, "$input" or die "$input: $!\n";
@ARGV = ('>&STDOUT') unless @ARGV;
my $output = shift @ARGV;
open my $out, ">$output" or die "$output: $!\n";

while (my $gff = <$in>) {
  chomp $gff;
  my @gff = split /\t/, $gff;
  $gff[0] =~ s/-OFFSET:(\d+)//;
  $gff[3] += $1;
  $gff[4] += $1;
  print $out join("\t", @gff), "\n";
}

=head1 SYNOPSIS:

 gffmapback.pl [OPTIONS] [infile [outfile]]

=head1 DESCRIPTION:

This script converts GFF lines with first entry in the format:
<ID>-OFFSET:<OFFSET> into just <ID> and adjusts the start and end
coordinates according to <OFFSET>.

=head1 OPTIONS:

=over 4

=item --help

Prints this help.

=back

=head1 EXAMPLES:

 gffmapback.pl infile.gff outfile.gff

 cat *.gff | gffbackmap.pl > outfile.gff

=head1 DEPENDENCIES:

 None.

=head1 AUTHOR:

Kasper Munch

=head1 COPYRIGHT:

This program is free software. You may copy, modify, and redistribute
it under the same terms as Perl itself.


=cut