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

[Scott Markel]

Brian,

The use case is when a user has many sequences to read and
is only interested in the sequence data for use in predicting
new features.  The user is likely to come back later and
look at some sequences in detail, so they only want to parse
the GenBank features then.  For the first pass, they would
like the reading sped up by omitting some of the parsing.

Scott

Brian Osborne wrote:

> Scott,
> 
> Why would you want to do this? I can imagine one reason, that there's some
> problem with a feature causing the script to exit. In that case do something
> like:
> 
> my $seq;
> eval { $seq = $seqIterator->next_seq; };
> 
> 
> Brian O.
> 
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Scott Markel
> Sent: Monday, January 17, 2005 9:00 PM
> To: Bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] possible to skip parsing features when
> callingBio::SeqIO::new?
> 
> 
> 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

-- 
Scott Markel, Ph.D.
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