[Biopython] 400 error, Did Entrez block me or is it something else?

[David Shin]

Thanks guys -

For now it eventually worked its way out, but if you could show me a
snippet of how try and except statements work, I would be thankful (I know
I can probably google it too), I'm also new to python in general, so coding
examples always help.

Thanks again,

Dave


On Thu, Dec 5, 2013 at 7:13 AM, <phyrexian.kavu at gmail.com> wrote:

> Hi David!
>
> I had the same error while trying to download hundreds of sequences from
> Entrez.efetch, I'm afraid this error cannot be resolved, since as Peter
> says it is an internet error. I avoided it by making a loop and adding the
> try - except statements, so whenever this error appeared, the script just
> returned and tried it again until the sequences were downloaded correctly.
> I know it is a brute force-like approach, but this was the best solution I
> could think of, I hope It helps you too.
>
> Miguel
>
>
> [Theropoda is my profession]
>
> > On 05/12/2013, at 06:31, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> >
> > Hi David,
> >
> > This is probably an intermittent failure, perhaps the NCBI
> > is very busy or there could be a temporary network problem
> > somewhere. The chances are it will work tomorrow...
> >
> > Peter
> >
> >
> >> On Thu, Dec 5, 2013 at 12:05 PM, David Shin <davidsshin at lbl.gov> wrote:
> >> Hi all -
> >>
> >> During off peak times, I was working on a script that takes a list of gi
> >> numbers (a list of 8) for protein sequences to use as input to get fasta
> >> sequences via Entrez.efetch. I passed along my email address during the
> >> searches. I am still new to python, etc. so had been testing my program.
> >>
> >> At some point I started getting the error below, and I'm not sure if it
> is
> >> my program, my web provider, or if ncbi got mad at me. It's been like
> this
> >> for about an hour, so giving up for the night.
> >>
> >> Thanks
> >>
> >> error:
> >>
> >> Traceback (most recent call last):
> >>  File "../gi-to-fasta5.py", line 11, in <module>
> >>    handle = Entrez.efetch(db="protein", rettype="fasta", retmode="text",
> >> id=gi_numbers)
> >>  File
> >> "/Users/daanac/onda/lib/python2.7/site-packages/Bio/Entrez/__init__.py",
> >> line 144, in efetch
> >>    return _open(cgi, variables, post)
> >>  File
> >> "/Users/daanac/onda/lib/python2.7/site-packages/Bio/Entrez/__init__.py",
> >> line 460, in _open
> >>    raise exception
> >> urllib2.HTTPError: HTTP Error 400: Bad Request
> >>
> >>
> >>
> >>
> >>
> >> --
> >> David Shin, Ph.D
> >> Lawrence Berkeley National Labs
> >> 1 Cyclotron Road
> >> MS 83-R0101
> >> Berkeley, CA 94720
> >> USA
> >> _______________________________________________
> >> Biopython mailing list  -  Biopython at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biopython
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
David Shin, Ph.D
Lawrence Berkeley National Labs
1 Cyclotron Road
MS 83-R0101
Berkeley, CA 94720
USA