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

[Karin Lagesen]

IIRC, NCBI requires a 3 second delay between fetches to avoid flooding 
the server. I cannot find again the site where I found this, but that's 
what I learned the last time I did this, and I am also finding the same 
info in bioperl documentation.

Karin

On 06.12.2013 08:20, David Shin wrote:
> 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
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>>
>
>
>


-- 
Karin Lagesen, Ph.D.
Department of Medical Genetics
and Norwegian High-Throughput Sequencing Centre (NSC)
Oslo University Hospital