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"""
This module is part of PythonCyc, a Python interface module to Pathway Tools.
This code has been tested with Python 2.6.
Pathway Tools (version 18.5 and up) must be running on some machine
with at least the option '-python'. It is also recommended
to start Pathway Tools with the option -lisp, so that the
connection can be monitored:
./pathway-tools -lisp -python
The global functions defined in this init file can be called before any
PGDB (an organism database in Pathway Tools) has been selected.
In fact, two of these functions, select_organism and
its synonym so, are needed to "select" a PGDB by creating a PGDB object.
See class PGDB in PGDB.py for information about how to use a PGDB object.
Please consult the tutorial.html file, under directory doc, for more information
about how to use PythonCyc.
"""
from PGDB import PGDB
from PTools import sendQueryToPTools
[docs]def select_organism(orgid):
"""
Select an organism PGDB based on its unique organism id.
orgid: string, the unique organism id in Pathway Tools (e.g., ecoli, meta).
"""
return PGDB(orgid)
[docs]def so(orgid):
""" A synonym of method select_organism. """
return select_organism(orgid)
[docs]def all_orgids():
"""
Returns all organism unique ids (orgids) available
from the current running Pathway Tools.
"""
orgids = sendQueryToPTools('(all-orgids)')
return orgids
[docs]def biovelo(query):
"""
Execute a BioVelo query and return the result.
Parameters
query: a string, which is a BioVelo query.
Returns
Whatever the BioVelo query computes.
Example
bv('[(p, reactions-of-pathway(p)): p<-ecoli^^pathways]')
"""
return sendQueryToPTools('(biovelo "'+query+'")')
[docs]def bv(query):
"""
A synonym of method biovelo.
"""
return biovelo(query)
[docs]def run_fba(fileName):
"""
The function run_fba does not need to have an organism selected before
being used because the FBA input file provided as input can specify
the organism.
For the documentation of this function, see method run_fba
in file PGDB.py.
"""
return sendQueryToPTools('(python-run-fba "'+fileName+'")')