#!/usr/bin/perl

# Time-stamp: <2005-02-17 13:42:06 kasper>

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

SYNOPSIS:

 lfamerge.pl [OPTIONS] <infile1> [infile2 [outfile]]

DESCRIPTION:

This script mergers the predictions of two infiles containing the same
sequences in the same order. The merged predictions are returned
together with the sequence and labels from the first infile.

OPTIONS:

       --help
             Prints this help.

EXAMPLES:

 lfamerge.pl infile1.lfa infile2.lfa outfile.lfa

 cat infile2.lfa | lfamerge.pl infile1.lfa > outfile.lfa

DEPENDENCIES

 Classes LFasta and LFastaIO.

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;

my $input1 = shift @ARGV or die USAGE;
open my $in1, "$input1" or die "$input1: $!\n";
@ARGV = ('-') unless @ARGV;
my $input2 = shift @ARGV;
open my $in2, "$input2" or die "$input2: $!\n";
@ARGV = ('>&STDOUT') unless @ARGV;
my $output = shift @ARGV;
open my $out, ">$output" or die "$output: $!\n";

$in1 = LFastaIO->new(fh => $in1);
$in2 = LFastaIO->new(fh => $in2);
$out = LFastaIO->new(fh => $out);

while (my $lfa1 = <$in1>) {
  my $lfa2 = <$in2>;
  die unless $lfa1->id eq $lfa2->id and $lfa1->seq eq $lfa2->seq;
  my $preds1 = $lfa1->preds;
  my $preds2 = $lfa2->preds;
  my $newpreds = [@$preds1, @$preds2];
  $lfa1->preds($newpreds);
  print $out $lfa1;
}

=head1 SYNOPSIS:

 lfamerge.pl [OPTIONS] <infile1> [infile2 [outfile]]

=head1 DESCRIPTION:

This script mergers the predictions of two infiles containing the same
sequences in the same order. The merged predictions are returned
together with the sequence and labels from the first infile.

=head1 OPTIONS:

=over 4

=item --help

Prints this help.

=back

=head1 EXAMPLES:

 lfamerge.pl infile1.lfa infile2.lfa outfile.lfa

 cat infile2.lfa | lfamerge.pl infile1.lfa > outfile.lfa

DEPENDENCIES

 Classes LFasta and LFastaIO.

=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