#!/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 phastcons scores from a specified genome.

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


use warnings;
use strict;
use Maasha::Biopieces;
use Maasha::Filesys;
use Maasha::UCSC::Wiggle;


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


my ( $options, $in, $out, $phastcons_file, $phastcons_index, $index, $fh_phastcons, $scores, $record );

$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 => 'flank',  short => 'f', type => 'uint',   mandatory => 'no',  default => 0,     allowed => undef, disallowed => undef },
    ]   
);

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

$phastcons_file  = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/phastcons/$options->{ 'genome' }.pp";
$phastcons_index = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/phastcons/$options->{ 'genome' }.pp.index";

$index           = Maasha::UCSC::Wiggle::fixedstep_index_retrieve( $phastcons_index );
$fh_phastcons    = Maasha::Filesys::file_read_open( $phastcons_file );

if ( defined $options->{ "chr" } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) )
{
    $options->{ "beg" } -= 1;   # request is 1-based
    $options->{ "end" } -= 1;   # request is 1-based

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

    $scores = Maasha::UCSC::Wiggle::fixedstep_index_lookup( $index, $fh_phastcons, $options->{ "chr" }, $options->{ "beg" }, $options->{ "end" }, $options->{ "flank" } );

    $record->{ "CHR" }       = $options->{ "chr" };
    $record->{ "CHR_BEG" }   = $options->{ "beg" } - $options->{ "flank" };
    $record->{ "CHR_END" }   = $options->{ "end" } + $options->{ "flank" };
    
    $record->{ "PHASTCONS" }   = join ",", @{ $scores };
    $record->{ "PHAST_COUNT" } = scalar @{ $scores };  # DEBUG

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

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    if ( $record->{ "REC_TYPE" } eq "BED" )
    {
        $scores = Maasha::UCSC::Wiggle::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "flank" } );
    }
    elsif ( $record->{ "REC_TYPE" } eq "PSL" )
    {
        $scores = Maasha::UCSC::Wiggle::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $options->{ "flank" } );
    }
    elsif ( $record->{ "REC_TYPE" } eq "BLAST" )
    {
        $scores = Maasha::UCSC::Wiggle::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $options->{ "flank" } );
    }

    $record->{ "PHASTCONS" } = join ",", @{ $scores } if @{ $scores };
#    $record->{ "PHAST_COUNT" } = @{ $scores } if @{ $scores };  # DEBUG

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

close $fh_phastcons if $fh_phastcons;                                                                                                                                          

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


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


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


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


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


__END__