qseq2fq.pl

#!/usr/bin/env perl
# ___UNDOCUMENTED___

use warnings;
use strict;
use Data::Dumper;
use Carp;
use Getopt::Long;
use Pod::Usage;

my $DATA_HANDLE = 'ARGV';
my $output;
my $skip_bad    = 1;

# Grabs and parses command line options
my $result = GetOptions (
    'output|o=s'  => \$output,
    'skip-bad|s'  => \$skip_bad,
    'verbose|v'   => sub { use diagnostics; },
    'quiet|q'     => sub { no warnings; },
    'help|h'      => sub { pod2usage ( -verbose => 1 ); },
    'manual|m'    => sub { pod2usage ( -verbose => 2 ); }
);

# Check required command line parameters
pod2usage ( -verbose => 1 )
unless @ARGV and $result;

if ($output) {
    open my $USER_OUT, '>', $output or croak "Can't open $output for writing: $!";
    select $USER_OUT;
}

READ:
while (<$DATA_HANDLE>) {

    chomp;

    my ($source, undef, $lane, $segment,
        $position, $read_number, undef,
        $read_pair, $sequence, $quality,
        $filtering) = split /\t/;
        
    next READ if $skip_bad && !$filtering;

    my $identifier = join (q{:},
                           $source, $lane, $segment,
                           $position, $read_number
                       ) . qq{/$read_pair};
    
    print join ("\n",
                qq{\@$identifier},
                $sequence,
                qq{+$identifier},
                $quality,
            ), "\n";
}


__END__


=head1 NAME

 name.pl - Short description

=head1 SYNOPSIS

=head1 DESCRIPTION

=head1 OPTIONS

 name.pl [OPTION]... [FILE]...

 -o, --output      filename to write results to (defaults to STDOUT)
 -v, --verbose     output perl's diagnostic and warning messages
 -q, --quiet       supress perl's diagnostic and warning messages
 -h, --help        print this information
 -m, --manual      print the plain old documentation page

=head1 REVISION

 Version 0.0.1

 $Rev: 249 $:
 $Author: psilva $:
 $Date: 2010-01-11 21:24:34 -0800 (Mon, 11 Jan 2010) $:
 $HeadURL: http://dzlab.pmb.berkeley.edu/svn/bisulfite/trunk/qseq2fq.pl $:
 $Id: qseq2fq.pl 249 2010-01-12 05:24:34Z psilva $:

=head1 AUTHOR

 Pedro Silva <psilva@nature.berkeley.edu/>
 Zilberman Lab <http://dzlab.pmb.berkeley.edu/>
 Plant and Microbial Biology Department
 College of Natural Resources
 University of California, Berkeley

=head1 COPYRIGHT

 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.

 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.

 You should have received a copy of the GNU General Public License
 along with this program. If not, see <http://www.gnu.org/licenses/>.

=cut