[Bioperl-l] get_Stream_by_acc in DB/GenBank.pm

[Jason Stajich]

Yes there is a bug in the older (0.7.2) version that was not parsing out
the <pre> tags properly and only took the last sequence.  In fact this bug
affects all the GenBank retrieval because the bad logic in the <pre>
parsing when there are multiple sequences retrieved for a single
accession.  This is because the Entrez queries are not asking specifically
for accession or gi (cause you can't do that with their interface). Use
Bio::DB::EMBL which uses the EBI dbfetch mechanism and is much more
reliable, but that is only available in 1.0... Hmm that doesn't help you.

You can have a local install of bioperl-1.0 in your dir and just
point your PERL5LIB to this (or add a use lib '/home/me/bioperl-1.0'
to the scripts that you want to use bioperl 1.0).   Now if you are doing
both Ensembl and Bioperl in the same script you're stuck.

-j

On Wed, 17 Apr 2002, Mick Watson wrote:

> Very quick, simple question....
>
> Are there known bugs in &get_Stream_by_acc in DB/GenBank.pm for BioPerl
> 0.7.2?
>
> Only if I use this method with two accession numbers, it tells me it is
> using this url to fetch the sequences:
>
>
> http://www.ncbi.nlm.nih.gov/entrez/utils/qmap.cgi?db=n&title=no&form=6&dopt=genbank&uid=BG295424,BI255773
>
> This url does indeed fetch the two sequences.  However, from the method
> call I only get one Bio::Seq object returned, and turning "-verbose" on
> in GenBank.pm reveals that only one GenBank record is being downloaded!
>
> I suspect this is a bug which has been fixed, but i don't want to
> upgrade Bioperl because I need this version for my local Ensembl to
> work....
>
> Thanks
> Mick
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu