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

Hilmar Lapp hlapp at gnf.org
Sat Feb 1 20:26:17 EST 2003

Probably genbank.pm should handle this. There is code in DB::GenBank  
redirecting to DB::RefSeq on certain accessions (CONTIGs I believe),  
but that's probably not applicable here.

Can you send me your patch?


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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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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