refactoring of assemble_pairs

[biopieces.git] / bp_bin / shuffle_seq

diff --git a/bp_bin/shuffle_seq b/bp_bin/shuffle_seq
index 05932c45e8f757bc87a2215272ab922697ddbfb6..009a785e4d728e2fb83daef080ebac44836a6a21 100755 (executable)
--- a/bp_bin/shuffle_seq
+++ b/bp_bin/shuffle_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;
@@ -43,29 +44,28 @@ $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
 
 while ( $record = Maasha::Biopieces::get_record( $in ) )
 {
-    $record->{ "SEQ" } = Maasha::Seq::seq_shuffle( $record->{ "SEQ" } ) if $record->{ "SEQ" };
+    $record->{ "SEQ" }    = Maasha::Seq::seq_shuffle( $record->{ "SEQ" } )    if $record->{ "SEQ" };
+    # $record->{ "SCORES" } = Maasha::Seq::seq_shuffle( $record->{ "SCORES" } ) if $record->{ "SCORES" }; # Hackery thing
 
     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();
 }