[Bioperl-l] SeqIO issue? EUtilities Cookbook

Peter biopython at maubp.freeserve.co.uk
Sat Mar 27 08:42:12 EDT 2010


On Fri, Mar 26, 2010 at 4:16 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Change the rettype from 'genbank' to 'gb' or 'gbwithparts' (the
> latter is if you always want a full nucleotide sequence instead
> of possibly getting contig files).  'genbank' used to be an alias
> for 'gb', but apparently no longer, and appears to be something
> that was changed on NCBI's end.

Yeah, the NCBI changed that almost a year ago (Easter 2009).
It broke one of the Biopython unit tests, and I asked the NCBI
about this and if they could restore the alias "genbank". They
declined, so in Biopython's efetch wrapper we spot anyone
asking for retype=genbank, issue a warning, and convert it
to retype=gb or retype=gp (for the protein database) instead.

The relevant Biopython code is here if anyone is interested:
http://biopython.org/SRC/biopython/Bio/Entrez/__init__.py

Peter



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