mistake: RE: [BioPython] TypeError: Unknown OP code: u'GROUP' and
other issues
Bonis Sanz, Julio
JBonis at imim.es
Tue Nov 30 10:27:36 EST 2004
There was an error in my code:
please replace this:
>> for db_id in db_ids:
>> #ids.append(db_id.dbids.ids[0]) #removed by jbonis
>> ids.append(int(db_id.records_dbids.ids[0])) #jbonis
>> return ids
with this:
>> for db_id in db_ids:
>> #ids.append(db_id.dbids.ids[0]) #removed by jbonis
>> ids.append(str(int(db_id.records_dbids.ids[0]))) #jbonis
>> return ids
( add a str to ids.append() ) ... it should work fine now
-----Mensaje original-----
De: biopython-bounces at portal.open-bio.org
[mailto:biopython-bounces at portal.open-bio.org]En nombre de Bonis Sanz,
Julio
Enviado el: martes, 30 de noviembre de 2004 16:14
Para: biopython at biopython.org
Asunto: [BioPython] TypeError: Unknown OP code: u'GROUP' and other
issues
Hi all,
Working with biopython I have found some bugs....
For example when using GenBank.search_for() function:
>> GenBank.search_for("HTR2A[GENE]")
it returns the error:
>> TypeError: Unknown OP code: u'GROUP'
This is becouse the XML from NCBI returns a "new" operator, named GROUP that is not included in the biopython code.
<TranslationStack>
<TermSet>
<Term>HTR2A[GENE]</Term>
<Field>GENE</Field>
<Count>27</Count>
<Explode>Y</Explode>
</TermSet>
<OP>GROUP</OP>
</TranslationStack>
I dont know what those operators means, but touching the biopython code (Bio/EUtils/parse.py) like this:
elif s == "NOT":
stack[-2:] = [Datatypes.Not(stack[-2], stack[-1])]
#added by jbonis
elif s == "GROUP":
garbage = s
#end of added by jbonis
else:
raise TypeError("Unknown OP code: %r" % (s,))
it works....
But there is other problem.... using GenBank.search_for() ... it returns:
"Error: Sequence Viewer does not have any Presentations for code='gi_text'"
the solution I have found is to change the Bio/GenBank/__init__py search_for() function like this:
>> for db_id in db_ids:
>> #ids.append(db_id.dbids.ids[0]) #removed by jbonis
>> ids.append(int(db_id.records_dbids.ids[0])) #jbonis
>> return ids
Hope it helps to others with the same problem, and to the people from biopython to improve the next release.
regards,
Julio Bonis Sanz MD
http://www.juliobonis.com/portal/
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