#!/usr/bin/perl

# Time-stamp: <2005-03-21 16:21:06 kasper>

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

SYNOPSIS:

 sumgff.pl [OPTIONS] [ infile [outfile] ]

DESCRIPTION:

This script sums the length of gfflines in a file or stream.

OPTIONS:

       --help
             Prints this help.
       --feature <regex>
             Sum only features with specified feature.

EXAMPLES:

 sumgff.pl file.gff output.txt

 cat file.gff | sumgff.pl output.txt

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;
my $feature = '.*';

GetOptions(
           "help" => \$help,
           "feature=s" => \$feature,
          ) 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";

my $sum = 0;
while (my $line = <$in>) {
  chomp $line;
  my @gff = split /\t/, $line;
  if ($gff[2] =~ /^$feature$/) {
    $sum += $gff[4] - $gff[3] + 1;
  }
}
print "$sum\n";

=head1 SYNOPSIS:

 sumgff.pl [OPTIONS] [ infile [outfile] ]

=head1 DESCRIPTION:

This script sums the length of gfflines in a file or stream.

=head1 OPTIONS:

=over 4

=item --help

Prints this help.

=item --feature <regex>

Sum only features with specified feature.

=back

=head1 EXAMPLES:

 sumgff.pl file.gff output.txt

 cat file.gff | sumgff.pl output.txt

=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