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Changing the database in lisp expression

asked 2017-08-23 10:34:49 -0500

jo gravatar image

updated 2017-08-24 01:59:37 -0500

I'm using sendQueryToPTools in PythonCyc in order to be able to use lisp expressions.

I can get the class of a pathway

pythoncyc.sendQueryToPTools("(get-instance-direct-types '|GLYSYN-PWY|)")

But this is not working for all pathways

pythoncyc.sendQueryToPTools("(get-instance-direct-types '|PWY-6120|)")

PToolsError: An internal error occurred in the running Pathway Tools application: :error Object "PWY-6120" is not coercible to a frame for KB ECOBASE

I assume it is caused by the database (ECOBASE). How can switch to METACYC?

PS.: I tried pythoncyc.select_organism('meta') but it is returning a pdgb object and seems to have no influence on the lisp query.

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answered 2017-08-29 23:09:39 -0500

I use a lisp command similar to:

(select-organism :org-id 'META)

incidentally, you can see what's in there with the command

(all-orgs)
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answered 2017-08-24 07:11:21 -0500

jo gravatar image

I found a workaround by starting the pathwaytools executable with metacyc as the default pgdb:

pathway-tools -python-local-only-non-strict -org META -lisp
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answered 2017-08-23 23:20:39 -0500

this post is marked as community wiki

This post is a wiki. Anyone with karma >75 is welcome to improve it.

Indeed, pathway PWY-6120 does not exist in EcoCyc. You can switch to MetaCyc by using the method pythoncyc.select_organism('meta'). For more information about this method, please see the documentation at http://pythoncyc.readthedocs.io/en/la....

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Unfortunately, this is not working. I used ``select_organism`` before sending the lisp query. I included this to the question

jo gravatar imagejo ( 2017-08-24 02:06:20 -0500 )edit

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Asked: 2017-08-23 10:34:49 -0500

Seen: 103 times

Last updated: Aug 29