[Biopython-dev] EFetch returning ASN.1 not genbank format

[Leighton Pritchard]

On 13/04/2009 18:55, "Peter" <biopython at maubp.freeserve.co.uk> wrote:

[...]
> I think we have two options:
> 
> (1) Add a special case to Bio.Entrez.eftech to map rettype="genbank"
> to rettype="gb" (or "gp" for the protein database).  This is simple
> and causes least disruption to Biopython uses, but is a bad idea in
> the long run as it means we are effectively providing our own variant
> of the Entrez API.
> 
> (2) Update our documentation and unit tests to use rettype="gb" or
> "gp" instead of rettype="genbank", and add a special case to
> Bio.Entrez.eftech to map rettype="genbank" to rettype="gb" (or "gp"
> for the protein database) and issue a warning that the NCBI have
> changed their API.  At a later point we might change this warning to
> an error.  This would provide a clear transition for end user scripts,
> and keep us consistent with the official Entrez API.
> 
> I favour option (2) here.  Any other thoughts?  Whatever we do should
> happen before we release Biopython 1.50.

Option (2).  Option (1) risks cementing an argument into place in Biopython
that could potentially contradict future Entrez API usage.

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
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