#!/usr/bin/env perl -w

# 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 EMBL entries from one or more files.

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


use strict;
use Maasha::Biopieces;
use Maasha::Filesys;
use Maasha::EMBL;


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


my ( $options, $in, $out, %options2, $file, $data_in, $num, $entry, $record );

$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 => 'keys',    short => 'k', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'feats',   short => 'f', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'quals',   short => 'q', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
    ]   
);

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

map { $options2{ "keys" }{ $_ } = 1 }  @{ $options->{ "keys" } };
map { $options2{ "feats" }{ $_ } = 1 } @{ $options->{ "feats" } };
map { $options2{ "quals" }{ $_ } = 1 } @{ $options->{ "quals" } };

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

if ( $options->{ 'data_in' } )
{
    $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );

    $num = 1;

    while ( $entry = Maasha::EMBL::get_embl_entry( $data_in ) ) 
    {
        $record = Maasha::EMBL::parse_embl_entry( $entry, \%options2 );

        my ( $feat, $feat2, $qual, $qual_val, $record_copy );

        $record_copy = dclone $record;

        delete $record_copy->{ "FT" };

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

        delete $record_copy->{ "SEQ" };

        foreach $feat ( keys %{ $record->{ "FT" } } )
        {
            $record_copy->{ "FEAT_TYPE" } = $feat;

            foreach $feat2 ( @{ $record->{ "FT" }->{ $feat } } )
            {
                foreach $qual ( keys %{ $feat2 } )
                {
                    $qual_val = join "; ", @{ $feat2->{ $qual } };

                    $qual =~ s/^_//;
                    $qual = uc $qual;

                    $record_copy->{ $qual } = $qual_val;
                }

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

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

        $num++;
    }

    close $data_in;
}


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


BEGIN
{
    $run_time_beg = Maasha::Biopieces::run_time();

    Maasha::Biopieces::log_biopiece();
}

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

    $run_time_end = Maasha::Biopieces::run_time();

    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
}


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


__END__