X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Falign_pair_seq;h=7f622f121d397cf0f124830860d3635935f94c5b;hb=c5233962d06d760ad5b5d32b30338fb30117b41b;hp=1f92640b15704b64900ebf52d4def7bdfc57a255;hpb=3424045c3eb23ca9da6241f33cdfa1dd629373db;p=biopieces.git

diff --git a/bp_bin/align_pair_seq b/bp_bin/align_pair_seq
index 1f92640..7f622f1 100755
--- a/bp_bin/align_pair_seq
+++ b/bp_bin/align_pair_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::AlignTwoSeq;
@@ -35,7 +36,7 @@ use Data::Dumper;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $count, $record, @records );
+my ( $options, $in, $out, $count, $record, @records, $space, $matches );
 
 $options = Maasha::Biopieces::parse_options();
 
@@ -54,11 +55,9 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
         if ( $count == 2 )
         {
-            $records[ 0 ]->{ 'SEQ' } = lc $records[ 0 ]->{ 'SEQ' };
-            $records[ 1 ]->{ 'SEQ' } = lc $records[ 1 ]->{ 'SEQ' };
-
-            my $matches = Maasha::AlignTwoSeq::align_two_seq( \$records[ 0 ]->{ 'SEQ' } ,\$records[ 1 ]->{ 'SEQ' } );
+            $matches = Maasha::AlignTwoSeq::align_two_seq( { 'Q_SEQ' => \$records[ 0 ]->{ 'SEQ' } , 'S_SEQ' => \$records[ 1 ]->{ 'SEQ' } }, [] );
             
+            Maasha::AlignTwoSeq::shift_case( $matches, \$records[ 0 ]->{ 'SEQ' } ,\$records[ 1 ]->{ 'SEQ' } );
             Maasha::AlignTwoSeq::insert_indels( $matches, \$records[ 0 ]->{ 'SEQ' } ,\$records[ 1 ]->{ 'SEQ' } );
 
             map { Maasha::Biopieces::put_record( $_, $out ) } @records;
@@ -70,26 +69,22 @@ 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();
 }
 
 
@@ -97,4 +92,3 @@ END
 
 
 __END__
-