adding bzip2 support in ruby

[biopieces.git] / bp_bin / blat_seq

diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq
index 00693022f4438c69c69a72a7801a4227fe9dfc06..1f327fab0997097901c1d060a46de4edc69062ff 100755 (executable)
--- a/bp_bin/blat_seq
+++ b/bp_bin/blat_seq
@@ -1,6 +1,6 @@
 #!/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
@@ -43,16 +43,17 @@ my ( $options, $in, $out, $record, $blat_args, $subject_file, $query_file, $fh_i
 
 $options = Maasha::Biopieces::parse_options(
     [
-        { 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 => '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 },
     ]   
 );
 
@@ -68,20 +69,15 @@ if ( $options->{ 'database' } ) {
     $subject_file = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna";
 }
 
-if ( $options->{ 'fast_map' } )
-{
-    $blat_args .= " -fastMap";
-}
-else
-{
-    $blat_args .= " -tileSize=$options->{ 'tile_size' }";
-    $blat_args .= " -oneOff=$options->{ 'one_off' }";
-    $blat_args .= " -minIdentity=$options->{ 'min_identity' }";
-    $blat_args .= " -minScore=$options->{ 'min_score' }";
-    $blat_args .= " -stepSize=$options->{ 'step_size' }";
-    $blat_args .= " -maxIntron=$options->{ 'intron_max' }";
-    # $blat_args .= " -ooc=" . Maasha::Config::genome_blat_ooc( $options->{ "genome" }, 11 ) if $options->{ 'ooc' };
-}
+$blat_args .= " -tileSize=$options->{ 'tile_size' }";
+$blat_args .= " -oneOff=$options->{ 'one_off' }";
+$blat_args .= " -minIdentity=$options->{ 'min_identity' }";
+$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 .= " -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();
 $query_file = "$tmp_dir/blat.seq";