[Biopython] Entrez and SeqIO "no records found in handle"

[A M Torres, Hugo]

This one bit me while following the cookbook tonight.

Explicitly setting retmode= 'xml' or 'html' fails.

I think I read somewhere that 'text' is expected to break every now and
then. Seems its the only retmode option that remains functional.

-- 
 .''`.      Hugo A. M. Torres
: :' :
`. `'   “Talk is cheap,
  `-    show me the code. ”  -- L. Torvalds.




2012/2/23 Peter Cock <p.j.a.cock at googlemail.com>

> 2012/2/23 高凤(Feng GAO) <fenggao0907 at yahoo.com.cn>:
> > Hi all,
> > We have some python code using gi number to get record from Genbank.
> > Part of the code is:
> >
> > handle = Entrez.efetch(db="protein", id=ID, rettype="gb")
> > record = SeqIO.read(handle,"genbank")
> >
> > We have had no problem with this code
> >  until this week when we started getting "ValueError: No records found
> in handle".
> > Anyone have an idea how to fix it now? Thanks!
> > Feng
>
> Try using an explicit retmode="text" in the efetch call.
> The NCBI changed the defaults with EFetch 2.0, which
> went live earlier this month. You're probably getting
> XML back instead.
>
> Note to self: I wonder if the Biopython tutorial examples
> need to be updated as well...
>
> Peter
>
>
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