[Bioperl-l] Re: SeqFeature::Annotated broken

[Allen Day]

i was hacking on this module yesterday.  i'll try to reproduce your error 
and get back to you.

-allen

On Fri, 19 Nov 2004, Scott Cain wrote:

> Allen,
> 
> 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,
>                     $feature->start,
>                     $feature->end)),"\n";
>   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?
> 
> Thanks,
> Scott
> 
> 
>