[Bioperl-guts-l] bioperl-live/Bio/SeqIO entrezgene.pm,1.17,1.18

Stefan Kirov skirov at pub.open-bio.org
Fri Mar 17 17:42:51 EST 2006


Update of /home/repository/bioperl/bioperl-live/Bio/SeqIO
In directory pub.open-bio.org:/tmp/cvs-serv12594/Bio/SeqIO

Modified Files:
	entrezgene.pm 
Log Message:
Capture KEGG pathway name


Index: entrezgene.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqIO/entrezgene.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** entrezgene.pm	19 Feb 2006 05:16:50 -0000	1.17
--- entrezgene.pm	17 Mar 2006 22:42:49 -0000	1.18
***************
*** 431,435 ****
          my $heading=$comm->{heading} || 'description';
          unless (exists($comm->{comment})) {
!             if (exists($comm->{type}) && exists($comm->{text}) && ($comm->{type} ne 'comment')) {
                  my ($uncapt,$annot,$anchor)=_process_src($comm->{source});
                  my $cann=shift (@$annot);
--- 431,438 ----
          my $heading=$comm->{heading} || 'description';
          unless (exists($comm->{comment})) {
! 		if (($comm->{type})&&($self->{_current_heading})) {
! 			$comm->{type}=$self->{_current_heading};
! 		}
!             if ((exists($comm->{type})) && (exists($comm->{text}))&& ($comm->{type} ne 'comment')) {
                  my ($uncapt,$annot,$anchor)=_process_src($comm->{source});
                  my $cann=shift (@$annot);
***************
*** 525,528 ****
--- 528,532 ----
      }
      if (@sfann) {push @{$cann{'dblink'}}, at sfann;}#Annotation that is not location specific, for example phenotype
+     undef $self->{_current_heading};
      return \@uncaptured,\%cann,\@feat;
  }
***************
*** 709,713 ****
  sub _process_all_comments {
  my $self=shift;
! my $product=$self->{_current};#Better without copying
  my @alluncaptured;
  my $heading=$product->{heading} if (exists($product->{heading}));
--- 713,717 ----
  sub _process_all_comments {
  my $self=shift;
! my $product=$self->{_current};#Better without copying 
  my @alluncaptured;
  my $heading=$product->{heading} if (exists($product->{heading}));
***************
*** 742,745 ****
--- 746,753 ----
                       push @alluncaptured,$self->_process_STS($product->{comment}); 
                       delete $product->{comment};
+                     last CLASS;
+                    }
+ 		   if ($heading =~ 'Pathways') {
+                      $self->{_current_heading}='Pathways';
                      last CLASS;
                     }



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