[Bioperl-guts-l] bioperl-live/Bio/Tools RepeatMasker.pm,1.4,1.5

Jason Stajich jason at pub.open-bio.org
Fri Nov 4 11:16:55 EST 2005


Update of /home/repository/bioperl/bioperl-live/Bio/Tools
In directory pub.open-bio.org:/tmp/cvs-serv25745/Bio/Tools

Modified Files:
	RepeatMasker.pm 
Log Message:
Emmanuel Quevillon's reported bug in creating feature2, I also simplified code into 2 new calls


Index: RepeatMasker.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/RepeatMasker.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** RepeatMasker.pm	17 Sep 2005 00:44:20 -0000	1.4
--- RepeatMasker.pm	4 Nov 2005 16:16:52 -0000	1.5
***************
*** 126,145 ****
              $strand = -1;
            }
!           my $rf = Bio::SeqFeature::Generic->new;
!           $rf->seq_id          ($query_name);
!           $rf->score            ($score);
!           $rf->start            ($query_start);
!           $rf->end              ($query_end);
!           $rf->strand           ($strand);
!           $rf->source_tag       ("RepeatMasker");
!           $rf->primary_tag      ($repeat_class);
!           my $rf2 = Bio::SeqFeature::Generic->new;
!           $rf2->seq_id         ($repeat_name);
!           $rf2->score           ($score);
!           $rf2->start           ($hit_start);
!           $rf2->end             ($hit_end);
!           $rf2->strand          ($strand);
!           $rf2->source_tag      ("RepeatMasker");
!           $rf->primary_tag      ($repeat_class);
            my $fp = Bio::SeqFeature::FeaturePair->new(-feature1=>$rf,
                                                       -feature2=>$rf2);
--- 126,147 ----
              $strand = -1;
            }
!           my $rf = Bio::SeqFeature::Generic->new
! 	      (-seq_id      => $query_name,
! 	       -score       => $score,
! 	       -start       => $query_start,
! 	       -end         => $query_end,
! 	       -strand      => $strand,
! 	       -source_tag  => 'RepeatMasker',
! 	       -primary_tag => $repeat_class);
! 
!           my $rf2 = Bio::SeqFeature::Generic->new
! 	      (-seq_id         => $repeat_name,
! 	       -score          => $score,
! 	       -start          => $hit_start,
! 	       -end            => $hit_end,
! 	       -strand         => $strand,
! 	       -source_tag     => "RepeatMasker",
! 	       -primary_tag    => $repeat_class);
! 
            my $fp = Bio::SeqFeature::FeaturePair->new(-feature1=>$rf,
                                                       -feature2=>$rf2);



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