[Bioperl-l] avoiding feature parsing

[Hilmar Lapp]

Excellent answer Marc. I was starting to look up the docs again but you 
were much faster.

	-hilmar

On Jun 10, 2005, at 5:05 PM, Marc Logghe wrote:

> Hi Danny,
>
>> my $seqio = Bio::SeqIO->new(-file => "$dir/$gi", -format => "fasta");
>>
>> and to my surprise it seems to parse the genbank files
>> correctly but only gets the sequence, which seems to solve
>> the problem.  My only question is "Is this the expected
>> behavior and can I rely on this working?  And.  Is their any
>
> Problem is, bioperl actually has parsed the complete gebank record,
> *including* the feature table. Of course, they do not show up in the
> fasta dump, but all features are attached to the sequence object
> anyways. This is the default behaviour.
> But you can say to the builder that you are not interested in the
> features.
>> From the perldoc of Bio::Seq::SeqBuilder:
>
> my $builder = $seqio->sequence_builder();
> # if you need only sequence, id, and description (e.g. for
> # conversion to FASTA format):
> $builder->want_none();
> $builder->add_wanted_slot('display_id','desc','seq');
>
> # if you want everything except the sequence and features
> $builder->want_all(1); # this is the default if it's untouched
> $builder->add_unwanted_slot('seq','features');
>
> HTH,
> Marc
>
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>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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