#!/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 SOFT entries from one or more files.
# http://www.ncbi.nlm.nih.gov/geo/info/soft2.html

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


use warnings;
use strict;
use Data::Dumper;
use Maasha::Biopieces;
use Maasha::Filesys;
use Maasha::NCBI;


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


my ( $options, $in, $out, $record, $data_in, $num, $entry, $records, $soft_index,
     $fh, @platforms, $plat_table, @samples, $sample, $old_end, $skip, $file );

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

$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 );
}

$num = 1;

foreach $file ( @{ $options->{ "data_in" } } )
{
    print STDERR "Creating index for file: $file\n" if $options->{ "verbose" };

    $soft_index = Maasha::NCBI::soft_index_file( $file );

    # print STDERR Dumper( $soft_index ) if $options->{ "verbose" };

    $fh         = Maasha::Filesys::file_read_open( $file );

    @platforms  = grep { $_->{ "SECTION" } =~ /PLATFORM/ } @{ $soft_index };

    print STDERR "Getting platform tables for file: $file\n" if $options->{ "verbose" };

    $plat_table = Maasha::NCBI::soft_get_platform( $fh, $platforms[ 0 ]->{ "LINE_BEG" }, $platforms[ -1 ]->{ "LINE_END" } );

    @samples    = grep { $_->{ "SECTION" } =~ /SAMPLE/ } @{ $soft_index };

    $old_end    = $platforms[ -1 ]->{ "LINE_END" };

    foreach $sample ( @samples )
    {
        $skip = 0;
        $skip = 1 if ( $options->{ "samples" } and grep { $sample->{ "SECTION" } !~ /$_/ } @{ $options->{ "samples" } } );

        print STDERR "Getting samples for dataset: $sample->{ 'SECTION' }\n" if $options->{ "verbose" } and not $skip;

        $records = Maasha::NCBI::soft_get_sample( $fh, $plat_table, $sample->{ "LINE_BEG" } - $old_end - 1, $sample->{ "LINE_END" } - $old_end - 1, $skip );

        foreach $record ( @{ $records } )
        {
            Maasha::Biopieces::put_record( $record, $out );

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

            $num++;
        }

        $old_end = $sample->{ "LINE_END" };
    }

    close $fh;
}

NUM:

close $data_in if $data_in;
close $fh if $fh;

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


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


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


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


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


__END__