[Bioperl-l] Parsing GenBank files w/o Sequences

[Hilmar Lapp]

I applied Peter's patch (and modified it insignificantly). This problem  
should be fixed therefore in the main trunk.

Core people, any opinions on whether this should go into the 1.2 branch  
as well?

	-hilmar

On Saturday, February 1, 2003, at 08:42  AM, Peter Chines wrote:

> Hi,
>
> I'm new to Bioperl (wrote my first script two days ago), so I may be
> trying to do something the wrong way.  I want to read GenBank files  
> that
> have all of the sequence features annotated, but don't actually have  
> any
> sequence, e.g. files like
> ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/H_sapiens/CHR_22/ 
> hs_chr22.gbs.gz
>
> Thanks to the wiki pages, I quickly hit on Bio::SeqIO and the sample
> code to read GenBank records.  Unfortunately, when there are multiple
> entries in a GenBank file, but no sequence for the records (no ORIGIN
> section), the parser skips over every other entry without any kind of
> warning message.
>
> Am I correct in thinking that Bio::SeqIO;;genbank should handle this
> type of GenBank record?  If so, I have a patch and some new tests to
> contribute--I'll send them to Elia unless someone else wants them.  If
> Bio::SeqIO;;genbank is not the best way to deal with these, please  
> point
> me toward the correct modules to use, and perhaps I'll look for a good
> place to document this.
>
> Thanks,
> Peter
>
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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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