[BioPython] genbank protein lookup issues

[Aaron Zschau]

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