[Bioperl-l] Data missing into Annotation object using Bio::SeqIO (Genbank)
Hilmar Lapp
hlapp at drycafe.net
Thu Jan 7 16:55:00 UTC 2010
I don't know to what extent this was followed up on further and I
guess it's too long ago to be of much help, but if it hasn't been
mentioned before I wanted to point out
Bio::SeqFeature::AnnotationAdaptor which integrates tag/value
annotation and Bio::Annotation annotation into one
AnnotationCollection, so it doesn't matter whether something is
attached as a tag or as an annotation object.
-hilmar
On Dec 16, 2009, at 10:09 AM, Chris Fields wrote:
> Emmanuel,
>
> The previous behavior in the 1.5.x series was to store feature tags
> as Bio::Annotation. The problem had been the way this was
> implemented was considered unsatisfactory for various reasons, so we
> reverted back to using simple tag-value pairs as the default. You
> can get at the data this way (from the Feature/Annotation HOWTO):
>
> for my $feat_object ($seq_object->get_SeqFeatures) {
> print "primary tag: ", $feat_object->primary_tag, "\n";
> for my $tag ($feat_object->get_all_tags) {
> print " tag: ", $tag, "\n";
> for my $value ($feat_object->get_tag_values($tag)) {
> print " value: ", $value, "\n";
> }
> }
> }
>
> You can also convert all the tag-value data into a
> Bio::Annotation::Collection using the
> Bio::SeqFeature::AnnotationAdaptor, but this is completely optional.
>
> chris
>
> On Dec 16, 2009, at 8:14 AM, Emmanuel Quevillon wrote:
>
>> Hi,
>>
>> I've wrote a small Genbank parser few months ago before BioPerl
>> release 1.6.0.
>> I tried to use my code once again but now the output of my parser
>> is empty.
>> It looks like Annotation from seqfeatures is not filled anymore.
>>
>> Here is the code I used previously:
>>
>> while(my $seq = $streamer->next_seq()){
>>
>> #We only want to retrieve CDS features...
>> foreach my $feat (grep { $_->primary_tag() eq 'CDS' } $seq-
>> >get_SeqFeatures()){
>> print $ofh join("#",
>> $feat->annotation()-
>> >get_Annotations('locus_tag'), # Acc num
>> $feat->annotation()->get_Annotations('gene')
>> ? $feat->annotation()-
>> >get_Annotations('gene') # Gene name
>> : $feat->annotation()-
>> >get_Annotations('locus_tag'),
>> $feat->annotation()-
>> >get_Annotations('product'), # Description
>> ),"\n";
>> }
>> }
>>
>> $feat is a Bio::SeqFeature::Generic object
>>
>> If I print Dumper($feat->annotation()) here is the output :
>>
>> $VAR1 = bless( {
>> '_typemap' => bless( {
>> '_type' => {
>> 'comment' =>
>> 'Bio::Annotation::Comment',
>> 'reference' =>
>> 'Bio::Annotation::Reference',
>> 'dblink' =>
>> 'Bio::Annotation::DBLink'
>> }
>> },
>> 'Bio::Annotation::TypeManager' ),
>> '_annotation' => {}
>> }, 'Bio::Annotation::Collection' );
>>
>> Have some changes been made into the way annotation object is
>> populated?
>>
>> Thanks for any clue and sorry if my question look stupid
>>
>> Regards
>>
>> Emmanuel
>>
>> --
>> -------------------------
>> Emmanuel Quevillon
>> Biological Software and Databases Group
>> Institut Pasteur
>> +33 1 44 38 95 98
>> tuco at_ pasteur dot fr
>> -------------------------
>>
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>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
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--
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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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