#!/usr/bin/env perl

# Copyright (C) 2007-2009 Martin A. Hansen.

# 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 2
# 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, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

# http://www.gnu.org/copyleft/gpl.html


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Scan sequences in the stream for restriction enzyme cleavage sites.

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


use warnings;
use strict;
use Data::Dumper;
use Maasha::RestrictEnz;
use Maasha::Biopieces;
use Maasha::Patscan;


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


my ( $options, $in, $out, $record, $re_data, $re, $matches, $match, %re_hash, $res_enz, $new_record );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'res_enz',      short => 'r', type => 'list',  mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'res_enz_in',   short => 'R', type => 'file!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'res_enz_only', short => 'o', type => 'flag',  mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'no_matches',   short => 'M', type => 'flag',  mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
    ]   
);

$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );

$re_data = Maasha::RestrictEnz::parse_re_data();

if ( $options->{ 'res_enz_in' } ) {
    $res_enz = Maasha::Patscan::read_patterns( $options->{ "res_enz_in" } );
}

push @{ $res_enz }, @{ $options->{ 'res_enz' } } if defined $options->{ 'res_enz' };

map { $re_hash{ $_ } = 1 } @{ $res_enz };

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    if ( $record->{ 'SEQ' } )
    {
        foreach $re ( @{ $re_data } )
        {
            next if not exists $re_hash{ $re->{ 'name' } };

            $matches = Maasha::RestrictEnz::re_scan( $record->{ 'SEQ' }, $re );

            %{ $new_record }              = %{ $record } if not $options->{ 'res_enz_only' };
            $new_record->{ 'RE' }         = $re->{ 'name' };
            $new_record->{ 'RE_COUNT' }   = scalar @{ $matches };
            $new_record->{ 'RE_MATCHES' } = join( ";", @{ $matches } ) if not $options->{ 'no_matches' };

            Maasha::Biopieces::put_record( $new_record, $out );
        }
    }

    # Maasha::Biopieces::put_record( $record, $out );
}

Maasha::Biopieces::close_stream( $in );
Maasha::Biopieces::close_stream( $out );


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


BEGIN
{
    Maasha::Biopieces::status_set();
}


END
{
    Maasha::Biopieces::status_log();
}


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


__END__