[Bioperl-l] possible to skip parsing features when calling Bio::SeqIO::new?

[Scott Markel]

Jason,

Excellent!  Thank you.

Scott

Jason Stajich wrote:

> See the docs for Bio::Seq::SeqBuilder
> 
> I think this will work:
> my $seqIterator = Bio::SeqIO->new("-file"   => "$file",
>                                     "-format" => "genbank");
> $seqIterator->sequence_builder->add_unwanted_slot('features');
> 
> If you additionally don't want the Annotations (references,etc)
> $seqIterator->sequence_builder->add_unwanted_slot('features', 
> 'annotation');
> 
> [don't ask why one is plural and other singular... =)]
> 
> -jason
> On Jan 17, 2005, at 9:00 PM, Scott Markel wrote:
> 
>> I'm using BioPerl 1.4 to read a GenBank sequence file.  Is there
>> an option or parameter I can set in the
>>
>> my $::seqIterator = Bio::SeqIO->new("-file"   => "$file",
>>                                     "-format" => "genbank");
>>
>> call that will cause the parser to skip the features?
>>
>> I checked BioPerl 1.5RC2 and didn't see any changes there
>> that would address my question.
>>
>> Scott
>>
> -- 
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
> 
> 

-- 
Scott Markel, Ph.D.
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