#!/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 EMBL files and output a file index.

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


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


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


my ( $options, $in, $out, $record, $file, $data_in, $entry, $id, $offset );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'data_in', short => 'i', type => 'files!', 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 );
}

foreach $file ( @{ $options->{ 'data_in' } } )
{
    Maasha::Common::error( qq(File "$file" is gzipped) ) if Maasha::Filesys::is_gzipped( $file );

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

    $offset = 0;

    while ( $entry = Maasha::EMBL::get_embl_entry( $data_in ) ) 
    {
        if ( $entry =~ /^ID   ([^;]+)/ )
        {
            $id = $1;

            $record = {
                FILE   => "$ENV{ 'PWD' }/$file",
                ID     => $id,
                OFFSET => $offset,
                LEN    => length $entry,
            };

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

            $offset += length $entry;
        }
        else
        {
            Maasha::Common::error( "Bad EMBL entry" );
        }
    }

    close $data_in;
}

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


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


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


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


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


__END__