refactoring of assemble_pairs

[biopieces.git] / bp_bin / transliterate_seq

diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq
index 9e10b65cd783bd5e7d7349915a1631fbd8dfb690..14dcb299f9ee0aecbd71af38fab9781119138941 100755 (executable)
--- a/bp_bin/transliterate_seq
+++ b/bp_bin/transliterate_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;
 
@@ -33,7 +34,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $search, $replace, $delete );
+my ( $options, $in, $out, $record, $search, $replace, $delete );
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -58,32 +59,30 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
             eval "\$record->{ 'SEQ' } =~ tr/$search/$replace/";
         } elsif ( $delete ) {
             eval "\$record->{ 'SEQ' } =~ tr/$delete//d";
+
+            $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
         }
     }
 
     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();
 }
 
 
@@ -91,4 +90,3 @@ END
 
 
 __END__
-