X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fread_stockholm;h=597e9e9b72f867636fea7593db052e4211610520;hb=48bea5c28b89dc5586d0bddb338ccd6ba23aa1f9;hp=530ddd4bcb1c52e785da3aa682c2a27cf6a0512e;hpb=fc6aa2a75a62c9da33195bbdf058c425235fe00c;p=biopieces.git

diff --git a/bp_bin/read_stockholm b/bp_bin/read_stockholm
index 530ddd4..597e9e9 100755
--- a/bp_bin/read_stockholm
+++ b/bp_bin/read_stockholm
@@ -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::Filesys;
@@ -35,7 +36,7 @@ use Maasha::Stockholm;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $num, $entry, $data_in, $record_anno, $key, $seq, $record_align );
+my ( $options, $in, $out, $record, $num, $entry, $data_in, $record_anno, $key, $seq, $record_align );
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -91,6 +92,8 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -98,19 +101,13 @@ if ( $options->{ 'data_in' } )
 
 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();
 }