latendre
commented
6 years ago Hello Pablo,
The Lisp (Pathway Tools) function pathway-components unfortunately breaks on pathways that are super-pathways, that is, pathways that have sub-pathways. You can directly see the issue by calling the pathway-components function, on a Lisp prompt, with the pwy-6883 as an argument. Therefore, before calling pathway-components you have to make sure that the pathway is not a super-pathway. One way to do that is to use the PythonCyc method all_pathways with the parameter “base" set to True. You will only have the base pathways returned. See the PythonCyc API for more details.
Best,
— Mario Latendresse SRI International
On Oct 16, 2018, at 9:25 AM, Pablo Peña notifications@github.com wrote:
I am sometimes getting a PToolsError when I am retrieving the components of a pathway. For example:
import pythoncyc meta = pythoncyc.select_organism('meta') pathway = meta['| PWY-6883|'] components = meta.pathway_components(pathway)
Throws this error:
Traceback (most recent call last): File "", line 1, in File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pythoncyc/PGDB.py", line 1441, in pathway_components return self.sendPgdbFnCall('pathway-components', may_be_frameid(pwy), **kwargs) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pythoncyc/PGDB.py", line 370, in sendPgdbFnCall return self.sendPgdbQuery(fnCall) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pythoncyc/PGDB.py", line 341, in sendPgdbQuery return PTools.sendQueryToPTools('(with-organism (:org-id ''+self._orgid+') '+query+')') File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pythoncyc/PTools.py", line 182, in sendQueryToPTools raise PToolsError('An internal error occurred in the running Pathway Tools application: %s' % r) pythoncyc.PTools.PToolsError: An internal error occurred in the running Pathway Tools application: :error, During the evaluation of '(WITH-ORGANISM (:ORG-ID 'META) (PATHWAY-COMPONENTS 'PWY-6883))', the following error occurred: #<TYPE-ERROR @
x1042840b32>
This happens every time I call meta.pathways_components for this pathway. This also occurs when I pass in the pathway frameid instead of the PFrame.
This error does not only happen to just this pathway, it happens to 390 other pathways. I got this number by running this code:
import pythoncyc meta = pythoncyc.select_organism('meta') pathways = meta.pathways cnt = 0
for pathway in pathways.instances: frameid = pathway.frameid try: components = meta.pathway_components(frameid) except: cnt = cnt + 1
print(cnt)
Why is this happening? Am I doing something wrong?
(Sorry about the indentation)
Hi dkaplan65 :) I hope that this is not too late, perhaps this might help you
import pythoncyc pathway_connection = pythoncyc.select_organism('meta')
retrieving all the available meta ids for the class "Pathways"
pathways_meta_ids = pathway_connection.get_class_all_instances("|Pathways|")
retrieving and appending to the list all the subclasses meta ids for the
class "Pathways"
pathways_meta_ids.extend(pathway_connection.get_class_all_subs("|Pathways|"))
Removing all the repeated pathway ids, if any
pathways_meta_ids = list(set(pathways_meta_ids))
looping through the pathways ids and trying to retrieve the components
for each pathway id
for pathway_id in pathways_meta_ids: print pathway_id, try: print pathway_connection.pathway_components(pathway_id) except: print "could not retrieve pathway components" If you have any issue or concern about how to use pythoncyc I might be able to help you, since I got a little experience with this library.
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I am sometimes getting a PToolsError when I am retrieving the components of a pathway. For example:
import pythoncycmeta = pythoncyc.select_organism('meta')pathway = meta['| PWY-6883|']components = meta.pathway_components(pathway)Throws this error:
This happens every time I call meta.pathways_components for this pathway. This also occurs when I pass in the pathway frameid instead of the PFrame.
This error does not only happen to just this pathway, it happens to 390 other pathways. I got this number by running this code:
import pythoncycmeta = pythoncyc.select_organism('meta')pathways = meta.pathwayscnt = 0for pathway in pathways.instances:frameid = pathway.frameidtry:components = meta.pathway_components(frameid)except:cnt = cnt + 1print(cnt)Why is this happening? Am I doing something wrong?
(Sorry about the indentation)