X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fwrite_psl;h=776676d782a8d80202c4293130e111bf7d3a0bd4;hb=2f0fd91b461033529a4a72e161bd133252a22eb6;hp=975b3692a2c44aead630be9075af2e714b1ac46c;hpb=61ede0a4aa00bb7770243d573872562bdc878524;p=biopieces.git

diff --git a/bp_bin/write_psl b/bp_bin/write_psl
index 975b369..776676d 100755
--- 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;
@@ -34,7 +35,7 @@ use Maasha::UCSC::PSL;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $fh, $record, @output, $first );
+my ( $options, $in, $out, $fh, $record, @output, $first );
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -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();
 }