refactoring of assemble_pairs

[biopieces.git] / bp_bin / write_psl

diff --git a/bp_bin/write_psl b/bp_bin/write_psl
index 43c85d485af0313dc43771328395eb0619944ef4..776676d782a8d80202c4293130e111bf7d3a0bd4 100755 (executable)
--- a/bp_bin/write_psl
+++ b/bp_bin/write_psl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::UCSC::PSL;
@@ -57,33 +58,30 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
     if ( $record->{ "REC_TYPE" } and $record->{ "REC_TYPE" } eq "PSL" )
     {
-        Maasha::UCSC::psl_put_header( $fh ) if $first;
-        Maasha::UCSC::psl_put_entry( $record, $fh );
+        Maasha::UCSC::PSL::psl_put_header( $fh ) if $first;
+        Maasha::UCSC::PSL::psl_put_entry( $record, $fh );
         $first = 0;
     }
 }
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }