[Bioperl-guts-l] [15008] bioperl-live/trunk: Fixes for the change to Bio::Annotation:: Comment that removed double quote overloading

[Scott Cain]

Revision: 15008
Author:   scain
Date:     2008-11-21 16:33:42 -0500 (Fri, 21 Nov 2008)

Log Message:
-----------
Fixes for the change to Bio::Annotation::Comment that removed double quote overloading

Modified Paths:
--------------
    bioperl-live/trunk/Bio/Tools/GFF.pm
    bioperl-live/trunk/scripts/Bio-DB-GFF/genbank2gff3.PLS

Modified: bioperl-live/trunk/Bio/Tools/GFF.pm
===================================================================
--- bioperl-live/trunk/Bio/Tools/GFF.pm	2008-11-21 16:36:46 UTC (rev 15007)
+++ bioperl-live/trunk/Bio/Tools/GFF.pm	2008-11-21 21:33:42 UTC (rev 15008)
@@ -1035,6 +1035,9 @@
 	for my $value ( $feat->each_tag_value($tag) ) {	    
 	    if(  defined $value && length($value) ) { 
 				#$value =~ tr/ /+/;  #spaces are allowed now
+                if ( ref $value eq 'Bio::Annotation::Comment') {
+                    $value = $value->text;
+                }
 
 		if ($value =~ /[^a-zA-Z0-9\,\;\=\.:\%\^\*\$\@\!\+\_\?\-]/) {
 		    $value =~ s/\t/\\t/g; # substitute tab and newline 

Modified: bioperl-live/trunk/scripts/Bio-DB-GFF/genbank2gff3.PLS
===================================================================
--- bioperl-live/trunk/scripts/Bio-DB-GFF/genbank2gff3.PLS	2008-11-21 16:36:46 UTC (rev 15007)
+++ bioperl-live/trunk/scripts/Bio-DB-GFF/genbank2gff3.PLS	2008-11-21 21:33:42 UTC (rev 15008)
@@ -670,7 +670,9 @@
       'dblink' => 'Dbxref',   
       'product' => 'product',
       'Reference' => 'reference',
-      'OntologyTerm' => 'Ontology_term', # stupid Cc_
+      'OntologyTerm' => 'Ontology_term',
+      'comment'  => 'Note',
+      'comment1' => 'Note',
       # various map-type locations
       # gene accession tag is named per source db !??
       # 'Index terms' => keywords ??
@@ -696,7 +698,11 @@
 
   foreach my $atag (sort keys %AnnotTagMap) {
     my $gtag= $AnnotTagMap{$atag}; next unless($gtag);
-    my @anno = map{ split( /[,;] */, "$_") if($_); } $seq->annotation->get_Annotations($atag);  
+    my @anno = map{ 
+          ref $_
+         ? split( /[,;] */, $_->value) 
+         : split( /[,;] */, "$_") if($_);
+         } $seq->annotation->get_Annotations($atag);  
     foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); }
     }