-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
-# Copyright (C) 2007-2009 Martin A. Hansen.
+# Copyright (C) 2007-2010 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
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+use warnings;
use strict;
use Maasha::Biopieces;
use Maasha::Filesys;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $options, $in, $out, $record, $blat_args, $genome_file, $query_file, $fh_in, $fh_out,
+my ( $options, $in, $out, $record, $blat_args, $subject_file, $query_file, $fh_in, $fh_out,
$tmp_dir, $type, $result_file, $entry );
$options = Maasha::Biopieces::parse_options(
[
- { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
- { long => 'fast_map', short => 'f', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'occ', short => 'c', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'intron_max', short => 'i', type => 'uint', mandatory => 'no', default => 750000, allowed => undef, disallowed => undef },
- { long => 'tile_size', short => 't', type => 'uint', mandatory => 'no', default => 11, allowed => undef, disallowed => 0 },
- { long => 'step_size', short => 's', type => 'uint', mandatory => 'no', default => 11, allowed => undef, disallowed => 0 },
- { long => 'min_identity', short => 'm', type => 'uint', mandatory => 'no', default => 90, allowed => undef, disallowed => 0 },
- { long => 'min_score', short => 'M', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
- { long => 'one_off', short => 'o', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'database', short => 'd', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'genome', short => 'g', type => 'genome', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'fast_map', short => 'f', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'occ', short => 'c', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'intron_max', short => 'i', type => 'uint', mandatory => 'no', default => 750000, allowed => undef, disallowed => undef },
+ { long => 'tile_size', short => 't', type => 'uint', mandatory => 'no', default => 11, allowed => undef, disallowed => 0 },
+ { long => 'step_size', short => 's', type => 'uint', mandatory => 'no', default => 11, allowed => undef, disallowed => 0 },
+ { long => 'min_identity', short => 'm', type => 'uint', mandatory => 'no', default => 90, allowed => undef, disallowed => 0 },
+ { long => 'min_score', short => 'M', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'one_off', short => 'o', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'allow_N_blocks', short => 'N', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
]
);
+Maasha::Common::error( qq(both --database and --genome specified) ) if $options->{ "genome" } and $options->{ "database" };
+Maasha::Common::error( qq(no --database or --genome specified) ) if not $options->{ "genome" } and not $options->{ "database" };
+
$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-$genome_file = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna";
+if ( $options->{ 'database' } ) {
+ $subject_file = $options->{ 'database' };
+} else {
+ $subject_file = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna";
+}
$blat_args .= " -tileSize=$options->{ 'tile_size' }";
$blat_args .= " -oneOff=$options->{ 'one_off' }";
$blat_args .= " -minScore=$options->{ 'min_score' }";
$blat_args .= " -stepSize=$options->{ 'step_size' }";
$blat_args .= " -maxIntron=$options->{ 'intron_max' }";
-$blat_args .= " -fastMap" if $options->{ 'fast_map' };
+$blat_args .= " -fastMap" if $options->{ 'fast_map' };
+$blat_args .= " -extendThroughN" if $options->{ 'allow_N_blocks' };
# $blat_args .= " -ooc=" . Maasha::Config::genome_blat_ooc( $options->{ "genome" }, 11 ) if $options->{ 'ooc' };
$tmp_dir = Maasha::Biopieces::get_tmpdir();
close $fh_out;
-$blat_args .= " -t=dnax" if $type eq "protein";
+$blat_args .= " -t=dnax" if $type eq "PROTEIN";
$blat_args .= " -q=$type";
$result_file = "$tmp_dir/blat.psl";
if ( $options->{ 'verbose' } ) {
- Maasha::Common::run( "blat", "$genome_file $query_file $blat_args $result_file" );
+ Maasha::Common::run( "blat", "$subject_file $query_file $blat_args $result_file" );
} else {
- Maasha::Common::run( "blat", "$genome_file $query_file $blat_args $result_file > /dev/null 2>&1" );
+ Maasha::Common::run( "blat", "$subject_file $query_file $blat_args $result_file > /dev/null 2>&1" );
}
unlink $query_file;