#!/usr/local/bin/perl

# Time-stamp: <2005-05-04 11:03:30 kasper>

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

SYNOPSIS:

 gff2table.pl [OPTIONS] [infile] [outfile]

DESCRIPTION:

This script makes a tab seperated table out of a gff line with lots of
messy stuff in the last column.

OPTIONS:

       --help
             Prints this help.

EXAMPLES:

 cat file.gff | gff2table.pl > file.table

 gff2table.pl file.gff file.table

AUTHOR:

Kasper Munch

COPYRIGHT:

This program is free software. You may copy 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 (<$in>) {
    $_ =~ /^((\S+\t){7}\S+)(.*)$/;
    print $out $1;
    my @att = split / ; /, $3;
    for (my $i = 0; $i < @att; $i++) {
        $att[$i] =~ s/^\s*\S+\s+/\t/;
        $att[$i] =~ s/\s+/\t/g if $i == 0;
        print $out "$att[$i]";
    }
    print $out "\n";
}

=head1 SYNOPSIS:

 gff2table.pl [OPTIONS] [infile] [outfile]

=head1 DESCRIPTION:

This script makes a tab seperated table out of a gff line with lots of
messy stuff in the last column.

=head1 OPTIONS:

=over 4

=item --help

Prints this help.

=back

=head1 EXAMPLES:

 cat file.gff | gff2table.pl > file.table

 gff2table.pl file.gff file.table

=head1 AUTHOR:

Kasper Munch

=head1 COPYRIGHT:

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


=cut