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

[David Shin]

Hi Karin,

Yes, I saw that in the tutorial manual, but appeared biopython took care of
that part. I was thinking about putting a delay in my script anyway.


On Fri, Dec 6, 2013 at 1:26 AM, Karin Lagesen
<karin.lagesen at medisin.uio.no>wrote:

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



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