[Bioperl-l] SeqFeature::Annotated broken

Scott Cain cain at cshl.org
Fri Nov 19 16:05:03 EST 2004


I think Bio::SeqFeature::Annotated is broken, though I am not really
sure.  When I run this test script:

#!/usr/bin/perl -w
use strict;

use lib '/home/scott/bioperl-live';
use Bio::FeatureIO;

my $in = Bio::FeatureIO->new(-file=> "test.gff", -format=>"gff");

while (my $feature = $in->next_feature()) {
  print join ("\t",($feature->display_name,
  my $ac = $feature->annotation;
  foreach my $key ($ac->get_all_annotation_keys() ) {
    my @values = $ac->get_Annotations($key);
    foreach my $value (@values) {
      print print "Annotation ",$key," stringified value ",$value->as_text,"\n";    }

and a small test GFF file, I get the following output:

-------------------- WARNING ---------------------
MSG: '##sequence-region' directive handling not yet implemented

-------------------- WARNING ---------------------
MSG: seq_id() is deprecated, use id()
Can't locate object method "remove_Annotations" via package "Bio::SeqFeature::Annotated" at /home/scott/bioperl-live/Bio/SeqFeature/Annotated.pm line 174, <GEN0> line 4.

Which is weird, because the remove_Annotations method is there.  Do you
have any insights as to what the problem might be?


Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

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