mfitzp / biocyc Goto Github PK

When trying the get method from the example:

o=biocyc.get('L-LACTATE')
o

I got the following error:

--------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-29-468f9bab9082> in <module>()
----> 1 o=biocyc.get('L-arginine')
      2 o

~\--\biocyc\biocyc.py in get(self, ids, skip_cache)
    397 
    398     def get(self, ids, skip_cache=False):
--> 399         return self.get_for_org(self.org_id, ids, skip_cache=skip_cache)
    400 
    401     def get_for_org(self, org_id, ids, skip_cache=False):

~\--\biocyc\biocyc.py in get_for_org(self, org_id, ids, skip_cache)
    423             if obj is None:
    424                 xml = self.request_obj(org_id, id)
--> 425                 obj = self.create_obj_from_xml(id, xml)
    426                 self.cache(obj) # Will cache either a real object, or a BioCycEntityNotFound
    427 

~\--\biocyc\biocyc.py in create_obj_from_xml(self, id, xml)
    442         for o in AVAILABLE_OBJECT_TYPES:
    443             if o.xml_schema_id:
--> 444                 x = xml.find(o.xml_schema_id)
    445                 if x: # Found it
    446                     # Create the base object, populating from the xml

AttributeError: 'bool' object has no attribute 'find'

Settings:
3.6.4 |Anaconda, Inc.| (default, Jan 16 2018, 10:22:32) [MSC v.1900 64 bit (AMD64)]

Maybe some sourcecode of BioCyc changed?

Hi, Thanks for this tool, I've been using it a lot :)

I tried to get the pathways for the ECOLI gene 'G7145' (the gene name is preT)
(I was able to get the pathways for many other genes but this one has a problem)
I can get the gene info using:

from biocyc import biocyc os.environ['http_proxy'] = '' # Set your proxy if neccessary biocyc.set_organism('ECOLI') gene_info = biocyc.get('G7145')

but when I try to get the pathways I get this error:

gene_info.pathway() returns:

AttributeError Traceback (most recent call last)
in
2 for gene_name in noisy_gene_names:
3 gene_info = biocyc.get(get_biocyc_gene_ID(gene_name))
----> 4 noisy_gene_pathway[gene_name] = gene_info.pathways
5

~\Anaconda3\lib\site-packages\biocyc\biocyc.py in pathways(self)
991 @Property
992 def pathways(self):
--> 993 return self.protein.pathways
994
995

~\Anaconda3\lib\site-packages\biocyc\biocyc.py in pathways(self)
960 # In case we're a subunit
961 for c in self.complexes:
--> 962 pathway_lists += [er.reaction.pathways for er in c.catalyzes]
963 return [p for pl in pathway_lists for p in pl]
964

~\Anaconda3\lib\site-packages\biocyc\biocyc.py in (.0)
960 # In case we're a subunit
961 for c in self.complexes:
--> 962 pathway_lists += [er.reaction.pathways for er in c.catalyzes]
963 return [p for pl in pathway_lists for p in pl]
964

~\Anaconda3\lib\site-packages\biocyc\biocyc.py in reaction(self)
871 @Property
872 def reaction(self):
--> 873 return biocyc.get_for_org( self.org_id, self._reaction )
874
875 @Property

~\Anaconda3\lib\site-packages\biocyc\biocyc.py in get_for_org(self, org_id, ids, skip_cache)
420 if obj is None:
421 xml = self.request_obj(org_id, id)
--> 422 obj = self.create_obj_from_xml(id, xml)
423 self.cache(obj) # Will cache either a real object, or a BioCycEntityNotFound
424

~\Anaconda3\lib\site-packages\biocyc\biocyc.py in create_obj_from_xml(self, id, xml)
439 for o in AVAILABLE_OBJECT_TYPES:
440 if o.xml_schema_id:
--> 441 x = xml.find(o.xml_schema_id)
442 if x: # Found it
443 # Create the base object, populating from the xml

AttributeError: 'bool' object has no attribute 'find'