def all_orgids():
"""
Returns all organism unique ids (orgids) available
from the current running Pathway Tools.
"""
orgids = sendQueryToPTools('(all-orgids)')
return orgids
def all_orgids():
"""
Returns all organism unique ids (orgids) available
from the current running Pathway Tools.
"""
orgids = sendQueryToPTools('(all-orgids)')
return orgids
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+'")')
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 + '")')
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+'")')
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 + '")')
