removed debug message

[biopieces.git] / bp_bin / translate_seq

diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq
index 445d5457ed893aaf83063b54df064389e29c561b..3af052136459dd53a6d5f01b994dc324fe614752 100755 (executable)
--- a/bp_bin/translate_seq
+++ b/bp_bin/translate_seq
@@ -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;
@@ -34,7 +35,7 @@ use Maasha::Seq;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $frame, %new_record );
+my ( $options, $in, $out, $record, $frame, %new_record );
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -49,7 +50,7 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 {
     if ( $record->{ "SEQ" } )
     {
-        if ( Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) eq "dna" )
+        if ( Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) eq "DNA" )
         {
             foreach $frame ( @{ $options->{ "frames" } } )
             {
@@ -69,26 +70,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     }
 }
 
+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();
 }
 
 
@@ -96,4 +93,3 @@ END
 
 
 __END__
-