X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fcalc_bit_scores;h=6da3afbddde48793a9ccd3ef43d5130fbb25f58b;hb=5de6112b70b59420b245ce636a8b2e3c90acbe00;hp=6bb5374eb2be9e55fe6c31c5aa6847f1071cbf8e;hpb=b607bb9d6e4adcebd9f9e128aacc91a212010ee0;p=biopieces.git

diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores
index 6bb5374..6da3afb 100755
--- a/bp_bin/calc_bit_scores
+++ b/bp_bin/calc_bit_scores
@@ -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::Seq;
@@ -68,7 +69,7 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 undef $record;
 
-if ( $type eq "protein" ) {
+if ( $type eq "PROTEIN" ) {
     $bit_max = 4;
 } else {
     $bit_max = 2;
@@ -85,25 +86,22 @@ for ( $i = 0; $i < keys %freq_hash; $i++ )
 
 Maasha::Biopieces::put_record( $record, $out );
 
+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();
 }
 
 
@@ -111,5 +109,3 @@ END
 
 
 __END__
-
-