fixes done to tmp_dir

[biopieces.git] / bp_bin / patscan_seq

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
index d6b9c1b60322b13824f5a25bc61f0d59d00a8f9b..611481c8123258ae574855c599dcaacf89fa943e 100755 (executable)
--- a/bp_bin/patscan_seq
+++ b/bp_bin/patscan_seq
@@ -28,6 +28,7 @@
 
 use strict;
 use Maasha::Biopieces;
+use Maasha::Common;
 use Maasha::Fasta;
 use Maasha::Filesys;
 use Maasha::Patscan;
@@ -41,8 +42,8 @@ use constant {
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $options, $in, $out, $record, @args, $arg, $type, $tmp_dir,
-     $seq_file, $pat_file, $out_file, $fh_in, $fh_out, $patterns, $pattern, $entry, $result, %head_hash, $i );
+my ( $options, $in, $out, $record, @args, $arg, $type, $tmp_dir, $seq_file, $pat_file, $out_file,
+     $fh_in, $fh_out, $patterns, $pattern, $entry, $result, %head_hash, $i );
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -104,7 +105,7 @@ foreach $pattern ( @{ $patterns } )
     pat_write( $pat_file, $pattern );
 
     `scan_for_matches $arg $pat_file < $seq_file > $out_file`;
-     # Maasha::Common::run( "scan_for_matches", "$arg $pat_file < $seq_file > $out_file" );
+#     Maasha::Common::run( "scan_for_matches", "$arg $pat_file < $seq_file > $out_file" );
 
     $fh_in = Maasha::Filesys::file_read_open( $out_file );
 
@@ -137,8 +138,6 @@ unlink $pat_file;
 unlink $out_file;
 unlink $seq_file if not $options->{ 'genome' };
 
-Maasha::Filesys::dir_remove( $tmp_dir );
-
 Maasha::Biopieces::close_stream( $in );
 Maasha::Biopieces::close_stream( $out );