From a8f2b8dbd9d579c56598b63a81cc6275ff4d6609 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 11 Feb 2010 16:35:57 +0000
Subject: [PATCH] added option for database search to blat_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@875 74ccb610-7750-0410-82ae-013aeee3265d
---
bp_bin/blat_seq | 34 +++++++++++++++++++++-------------
1 file changed, 21 insertions(+), 13 deletions(-)
diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq
index 220e7b3..073cfd8 100755
--- a/bp_bin/blat_seq
+++ b/bp_bin/blat_seq
@@ -38,27 +38,35 @@ use Maasha::UCSC::PSL;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-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 },
]
);
+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' }";
@@ -93,9 +101,9 @@ $blat_args .= " -q=$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;
--
2.39.5