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

# Create a BLAST database from sequences in stream for use with [blast_seq].

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


use warnings;
use strict;
use Maasha::Seq;
use Maasha::Fasta;
use Maasha::Biopieces;


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


my ( $options, $in, $out, $record, $tmp_dir, $file_tmp, $fh_tmp, $entry, $seq_type, $arg );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'no_stream',  short => 'x', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
        { long => 'directory',  short => 'd', type => 'dir',    mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
        { long => 'index_name', short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
    ]   
);

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

$tmp_dir  = Maasha::Biopieces::get_tmpdir();
$file_tmp = "$tmp_dir/$options->{ 'index_name' }";
$fh_tmp   = Maasha::Filesys::file_write_open( $file_tmp );

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
    {
        $seq_type = Maasha::Seq::seq_guess_type( $record->{ 'SEQ' } ) if not $seq_type;

        Maasha::Fasta::put_entry( $entry, $fh_tmp );
    }

    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
}

close $fh_tmp;

$arg = "-t $options->{ 'index_name' }";

if ( $seq_type eq "PROTEIN" ) {
    $arg .= " -p T";
} else {
    $arg .= " -p F";
}

$arg .= " -v 12000";
$arg .= " -i $file_tmp";

if ( $options->{ 'verbose' } )
{
    print STDERR "Running: formatdb $arg\n";

    Maasha::Common::run( "formatdb", "$arg" );
}
else
{
    Maasha::Common::run( "formatdb", "$arg -l /dev/null" );
}

Maasha::Filesys::dir_create_if_not_exists( $options->{ 'directory' } );

unlink $file_tmp;

system( "cp $tmp_dir/* $options->{ 'directory' }" );

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


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


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


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


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


__END__