#! /usr/bin/perl

# Time-stamp: <2004-10-27 11:18:34 kasper>

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

SYNOPSIS:

 seqfiletest.pl [OPTIONS] [infile [outfile]]

DESCRIPTION:

This script tests wether a created sequence file can be read and
written by the Bio::SeqIO obj. That is, whether it is syntactically
correct (in Bioperl's point of view).

OPTIONS:

       --format
             Format of inputfile.
       --help
             Prints this help.

EXAMPLES:

 cat file.embl | seqfiletest.pl

 seqfiletest.pl file.embl

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;
my $format = 'Fasta';

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

# Create a SeqIO obj. for input:
$in = Bio::SeqIO->newFh(-fh => $in, -format => $format );
# Create a the output file handle:
$out = Bio::SeqIO->newFh(-fh => $out, -format => $format );

while (<$in>) {
    print $out $_;
}

=head1 SYNOPSIS:

 seqfiletest.pl [OPTIONS] [infile [outfile]]

=head1 DESCRIPTION:

This script tests wether a created sequence file can be read and
written by the Bio::SeqIO obj. That is, whether it is syntactically
correct (in Bioperl's point of view).

=head1 OPTIONS:

=over 4

=item --format

Format of inputfile.

=item --help

Prints this help.

=back

=head1 EXAMPLES:

 cat file.embl | seqfiletest.pl

 seqfiletest.pl file.embl

=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