[Bioperl-guts-l] bioperl-live/t seqwithquality.t,1.6,1.7

Heikki Lehvaslaiho heikki at pub.open-bio.org
Thu Jul 7 12:16:17 EDT 2005


Update of /home/repository/bioperl/bioperl-live/t
In directory pub.open-bio.org:/tmp/cvs-serv19905/t

Modified Files:
	seqwithquality.t 
Log Message:
handle zero as a quality value, fix bug #1824


Index: seqwithquality.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/seqwithquality.t,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** seqwithquality.t	19 Dec 2002 22:10:34 -0000	1.6
--- seqwithquality.t	7 Jul 2005 16:16:15 -0000	1.7
***************
*** 166,179 ****
  		$swq1->seq_obj($seqobj);
  
! print("6. Testing the subqual() method...\n");
       my $t_subqual = "10 20 30 40 50 60 70 80 90";
       $swq1->qual($t_subqual);
!      print("\t6d) Testing the subqual at the start (border condition)\n");
            # ok ('1 2 3' eq join(' ',@{$swq1->subqual(1,3)}));
!      print("\t6d) Testing the subqual at the end (border condition)\n");
            # ok ('7 8 9' eq join(' ',@{$swq1->subqual(7,9)}));
!      print("\t6d) Testing the subqual in the middle\n");
            # ok ('4 5 6' eq join(' ',@{$swq1->subqual(4,6)}));
  
  
  
--- 166,194 ----
  		$swq1->seq_obj($seqobj);
  
! print("6. Testing the subqual() method...\n") if $DEBUG;
       my $t_subqual = "10 20 30 40 50 60 70 80 90";
       $swq1->qual($t_subqual);
!      print("\t6d) Testing the subqual at the start (border condition)\n") if $DEBUG;
            # ok ('1 2 3' eq join(' ',@{$swq1->subqual(1,3)}));
!      print("\t6d) Testing the subqual at the end (border condition)\n") if $DEBUG;
            # ok ('7 8 9' eq join(' ',@{$swq1->subqual(7,9)}));
!      print("\t6d) Testing the subqual in the middle\n") if $DEBUG;
            # ok ('4 5 6' eq join(' ',@{$swq1->subqual(4,6)}));
  
  
+ print("7. Testing cases where quality is zero...\n") if $DEBUG;
+ $swq1 = Bio::Seq::SeqWithQuality->new(-seq =>  'G',
+                                       -qual => '0',
+                                      );
+ my $swq2 = Bio::Seq::SeqWithQuality->new(-seq =>  'G',
+                                          -qual => '65',
+                                      );
+ ok  $swq1->length, $swq2->length;
  
+ $swq1 = Bio::Seq::SeqWithQuality->new(-seq =>  'GC',
+                                       -qual => '0 0',
+                                      );
+ my $swq2 = Bio::Seq::SeqWithQuality->new(-seq =>  'GT',
+                                          -qual => '65 0',
+                                      );
+ ok  $swq1->length, $swq2->length;



More information about the Bioperl-guts-l mailing list