[BioPython] genbank protein lookup issues

[Aaron Zschau]

I've managed to confirm that the problem line is as follows:

gi_list = GenBank.search_for("YAL038w",database='protein')

if I just take that one line out and run it by hand from the python  
prompt (with the necessary imports first), I get the following error:

 >>> gi_list = GenBank.search_for("YAL038w",database='protein')
Traceback (most recent call last):
   File "<stdin>", line 1, in ?
   File  
"/tmp/biopython-1.30/build/lib.linux-i586-2.2/Bio/GenBank/__init__.py",  
line 1398, in search_for
     retstart = start_id, retmax = max_ids)
   File "/usr/lib/python2.2/site-packages/Bio/EUtils/DBIdsClient.py",  
line 294, in search
     searchinfo = parse.parse_search(infile, [None])
   File  
"/tmp/biopython-1.30/build/lib.linux-i586-2.2/Bio/EUtils/parse.py",  
line 219, in parse_search
     raise TypeError("Unknown OP code: %r" % (s,))
TypeError: Unknown OP code: u'GROUP'



Does anybody know why this would be happening or if it is a known  
problem with the genbank servers/parsing?

thanks,

Aaron Zschau


On Nov 12, 2004, at 12:21 AM, Aaron Zschau wrote:

> Something seems to have broken since I last ran this program a few  
> weeks ago, my line:
>
> gi_list = GenBank.search_for(form["genename"].value,  
> database="protein")
>
> with values for form["genename"].value such as "YAL038w"  but it seems  
> to give the error no matter what search string I use. I haven't made  
> any changes to my code since it last worked so I'm wondering if  
> genbank changed something.
>
>
> I get the following errors in my logs from running:
>
> [Fri Nov 12 00:14:20 2004] [error] [client 10.0.10.22] Traceback (most  
> recent call last):, referer:  
> http://serval.atroxen.com:8080/interface.html
> [Fri Nov 12 00:14:20 2004] [error] [client 10.0.10.22]   File  
> "/var/www/cgi-bin/cluster.py", line 78, in ?, referer:  
> http://serval.atroxen.com:8080/interface.html
> [Fri Nov 12 00:14:20 2004] [error] [client 10.0.10.22]     gi_list =  
> GenBank.search_for(form["genename"].value, database="protein"),  
> referer: http://serval.atroxen.com:8080/interface.html
> [Fri Nov 12 00:14:20 2004] [error] [client 10.0.10.22]   File  
> "/tmp/biopython-1.30/build/lib.linux-i586-2.2/Bio/GenBank/ 
> __init__.py", line 1398, in search_for, referer:  
> http://serval.atroxen.com:8080/interface.html
> [Fri Nov 12 00:14:20 2004] [error] [client 10.0.10.22]     retstart =  
> start_id, retmax = max_ids), referer:  
> http://serval.atroxen.com:8080/interface.html
> [Fri Nov 12 00:14:20 2004] [error] [client 10.0.10.22]   File  
> "/usr/lib/python2.2/site-packages/Bio/EUtils/DBIdsClient.py", line  
> 294, in search, referer: http://serval.atroxen.com:8080/interface.html
> [Fri Nov 12 00:14:20 2004] [error] [client 10.0.10.22]     searchinfo  
> = parse.parse_search(infile, [None]), referer:  
> http://serval.atroxen.com:8080/interface.html
> [Fri Nov 12 00:14:20 2004] [error] [client 10.0.10.22]   File  
> "/tmp/biopython-1.30/build/lib.linux-i586-2.2/Bio/EUtils/parse.py",  
> line 219, in parse_search, referer:  
> http://serval.atroxen.com:8080/interface.html
> [Fri Nov 12 00:14:20 2004] [error] [client 10.0.10.22]     raise  
> TypeError("Unknown OP code: %r" % (s,)), referer:  
> http://serval.atroxen.com:8080/interface.html
> [Fri Nov 12 00:14:20 2004] [error] [client 10.0.10.22] TypeError:  
> Unknown OP code: u'GROUP', referer:  
> http://serval.atroxen.com:8080/interface.html
>
>
> any help would be appreciated,
>
> Aaron Zschau
>
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