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

# Use bowtie to map sequences in the stream against a specified genome.

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


use warnings;
use strict;
use Maasha::Biopieces;
use Maasha::Common;
use Maasha::Fastq;
use Maasha::Fasta;
use Maasha::Calc;


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


my ( $options, $in, $out, $index, $tmp_dir, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $entry, $line, @fields, $type, $args );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
    ]   
);

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

$index = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/bowtie/$options->{ 'genome' }";

$tmp_dir = Maasha::Biopieces::get_tmpdir();
$tmp_in  = "$tmp_dir/bowtie.seq";
$tmp_out = "$tmp_dir/bowtie.out";

$fh_out = Maasha::Filesys::file_write_open( $tmp_in );

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    if ( $entry = Maasha::Fastq::biopiece2fastq( $record ) )
    {
        Maasha::Common::error( "Mixed FASTA and FASTQ entries in stream" ) if defined $type and $type ne "FASTQ";
        Maasha::Fastq::put_entry( $entry, $fh_out );

        $type = "FASTQ";
    }
    elsif ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
    {
        Maasha::Common::error( "Mixed FASTA and FASTQ entries in stream" ) if defined $type and $type ne "FASTA";
        Maasha::Fasta::put_entry( $entry, $fh_out );

        $type = "FASTA";
    }

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

close $fh_out;

$args = "";
$args = "-f" if $type eq "FASTA";

if ( $options->{ 'verbose' } ) {
    Maasha::Common::run( "bowtie", "$args $index $tmp_in $tmp_out" );
} else {
    Maasha::Common::run( "bowtie", "$args $index $tmp_in $tmp_out > /dev/null 2>&1" );
}

unlink $tmp_in;

$fh_in = Maasha::Filesys::file_read_open( $tmp_out );

while ( $line = <$fh_in> )
{
    chomp $line;

    @fields = split /\t/, $line;

    $record = bowtie2biopiece( \@fields );

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

close $fh_out;

unlink $tmp_out;

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


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


sub bowtie2biopiece
{
    # Martin A. Hansen, July 2009

    # Convert a bowtie entry to a Biopiece record.

    my ( $entry,   # bowtie entry
       ) = @_;

    # Returns a hash.

    my ( $record, @scores );

    $record->{ 'Q_ID' }     = $entry->[ 0 ];
    $record->{ 'STRAND' }   = $entry->[ 1 ];
    $record->{ 'S_ID' }     = $entry->[ 2 ];
    $record->{ 'S_BEG' }    = $entry->[ 3 ];
    $record->{ 'SEQ' }      = $entry->[ 4 ];
    $record->{ 'SCORES' }   = $entry->[ 5 ];
    $record->{ 'MISMATCH' } = $entry->[ 6 ];

    $record->{ 'SEQ_LEN' }    = length $entry->[ 4 ];
    $record->{ 'S_END' }      = $record->{ 'S_BEG' } + $record->{ 'SEQ_LEN' } - 1;
    $record->{ 'SCORES' }     =~ s/(.)/ord( $1 ) - 33 . ";"/ge; # http://maq.sourceforge.net/fastq.shtml
    $record->{ 'SCORE_MEAN' } = sprintf( "%.2f", Maasha::Calc::mean( [ split /;/, $record->{ 'SCORES' } ] ) );

    $record->{ 'REC_TYPE' } = "BOWTIE";

    return wantarray ? %{ $record } : $record; 
}


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


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


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


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


__END__