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

# Extract alignments from a multiple genome alignment.

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


use warnings;
use strict;
use Maasha::Biopieces;
use Maasha::Common;
use Maasha::UCSC;


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


my ( $options, $in, $out, $record, $tmp_dir, $maf_track, $align, $align_num, $beg, $end, $len, $entry );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
        { long => 'chr',    short => 'c', type => 'string', mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
        { long => 'beg',    short => 'b', type => 'uint',   mandatory => 'no',  default => undef, allowed => undef, disallowed => 0     },
        { long => 'end',    short => 'e', type => 'uint',   mandatory => 'no',  default => undef, allowed => undef, disallowed => 0     },
        { long => 'len',    short => 'l', type => 'uint',   mandatory => 'no',  default => undef, allowed => undef, disallowed => 0     },
        { long => 'strand', short => 's', type => 'string', mandatory => 'no',  default => '+',   allowed => '+,-', disallowed => undef },
    ]   
);

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

$tmp_dir = Maasha::Biopieces::get_tmpdir();

$align_num = 1;

$maf_track = maf_track( $options->{ "genome" } );

if ( $options->{ "chr" } and $options->{ "beg" } and ( $options->{ "end" } or $options->{ "len" } ) )
{
    $beg = $options->{ "beg" } - 1;
    
    if ( $options->{ "end" } ) {
        $end = $options->{ "end" };
    } elsif ( $options->{ "len" } ) {
        $end = $beg + $options->{ "len" };
    }

    $align = Maasha::UCSC::maf_extract( $tmp_dir, $options->{ "genome" }, $maf_track, $options->{ "chr" }, $beg, $end, $options->{ "strand" } );

    foreach $entry ( @{ $align } )
    {
        $entry->{ "CHR" }     = $record->{ "CHR" };
        $entry->{ "CHR_BEG" } = $record->{ "CHR_BEG" };
        $entry->{ "CHR_END" } = $record->{ "CHR_END" };
        $entry->{ "STRAND" }  = $record->{ "STRAND" } || '+';
        $entry->{ "Q_ID" }    = $record->{ "Q_ID" };
        $entry->{ "SCORE" }   = $record->{ "SCORE" };

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

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    if ( $record->{ "REC_TYPE" } eq "BED" )
    {
        $align = Maasha::UCSC::maf_extract( $tmp_dir, $options->{ "genome" }, $maf_track, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $record->{ "STRAND" } );
    }
    elsif ( $record->{ "REC_TYPE" } eq "VMATCH" )
    {
        $align = Maasha::UCSC::maf_extract( $tmp_dir, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" } + 1, $record->{ "STRAND" } );
    }
    elsif ( $record->{ "REC_TYPE" } eq "PSL" )
    {
        $align = Maasha::UCSC::maf_extract( $tmp_dir, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $record->{ "STRAND" } );
    }
    elsif ( $record->{ "REC_TYPE" } eq "BLAST" )
    {
        $align = Maasha::UCSC::maf_extract( $tmp_dir, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $record->{ "STRAND" } );
    }

    foreach $entry ( @{ $align } )
    {
        $entry->{ "CHR" }     = $record->{ "CHR" };
        $entry->{ "CHR_BEG" } = $record->{ "CHR_BEG" };
        $entry->{ "CHR_END" } = $record->{ "CHR_END" };
        $entry->{ "STRAND" }  = $record->{ "STRAND" };
        $entry->{ "Q_ID" }    = $record->{ "Q_ID" };
        $entry->{ "SCORE" }   = $record->{ "SCORE" };

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

    $align_num++;
}

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


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


sub maf_track
{
    # Martin A. Hansen, April 2008.

    # Given a genome returns the corresponding mafTrack database table name.

    my ( $genome,   # genome to lookup.
       ) = @_;

    # Returns a string.

    my ( %hash );

    # The below has should be in a config file - fix later.

    %hash = (
        danRer4 => 'multiz7way',
        dm2     => 'multiz15way',
        dm3     => 'multiz15way',
        fr2     => 'multiz7way',
        galGal3 => 'multiz7way',
        gasAcu1 => 'multiz7way',
        hg18    => 'multiz17way',
        mm8     => 'multiz17way',
        mm9     => 'multiz17way',
        oryLat1 => 'multiz7way',
        panTro2 => 'multiz17way',
        tetNig1 => 'multiz7way',
    );

    Maasha::Common::error( qw(multiz track not found) ) if not exists $hash{ $genome };

    return $hash{ $genome };
}


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


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


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


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


__END__