#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Read nucleotide sequences in 2bit format from one or more files.

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


use warnings;
use strict;
use Maasha::Biopieces;
use Maasha::Filesys;
use Maasha::TwoBit;


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


my ( $options, $in, $out, $record, $file, $data_in, $mask, $toc, $line, $num );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'num',     short => 'n', type => 'uint',   mandatory => 'no', default => undef, allowed => undef, disallowed => '0'   },
        { long => 'no_mask', short => 'N', 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" } );

while ( $record = Maasha::Biopieces::get_record( $in ) ) {
    Maasha::Biopieces::put_record( $record, $out );
}

$mask = 1 if not $options->{ "no_mask" };

$num = 1;

foreach $file ( @{ $options->{ "data_in" } } )
{
    $data_in = Maasha::Filesys::file_read_open( $file );

    $toc = Maasha::TwoBit::twobit_get_TOC( $data_in );

    foreach $line ( @{ $toc } )
    {
        $record->{ "SEQ_NAME" } = $line->[ 0 ];
        $record->{ "SEQ" }      = Maasha::TwoBit::twobit_get_seq( $data_in, $line->[ 1 ], undef, undef, $mask );
        $record->{ "SEQ_LEN" }  = length $record->{ "SEQ" };

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

        goto NUM if $options->{ "num" } and $num == $options->{ "num" };

        $num++;
    }

    close $data_in;
}

NUM:

close $data_in if $data_in;

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


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


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


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


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


__END__