# needs: pathway-tools -python-local-only-non-strict -lisp
import pythoncyc
import sys
import re
import pdb
meta = pythoncyc.select_organism('meta')
pythoncyc.sendQueryToPTools("(select-organism :org-id 'META)")
def getReaInfos(pwy):
meta.allpwy = meta.all_pathways()
#pwy = "ANAEROFRUCAT-PWY"
#pwy = "ALL-CHORISMATE-PWY"
if meta[pwy] == None:
print(pwy, "Pathway does not exist")
return ([[], []])
rea_list = []
if meta[pwy].key_reactions != None:
keyRea_list = meta[pwy].key_reactions
else:
keyRea_list = []
check_list = meta[pwy]["reaction_list"]
if meta[pwy].sub_pathways != None:
check_list.extend(
[p for p in meta[pwy].sub_pathways if p not in check_list])
isSuperPwy = False
while len(check_list) > 0:
ptmp = check_list.pop()
# needs: pathway-tools -python-local-only-non-strict -lisp
import pythoncyc
meta = pythoncyc.select_organism('meta')
pythoncyc.sendQueryToPTools("(select-organism :org-id 'META)")
#query = "|Amino-Acid-Biosynthesis|"
#query = "|Nucleotide-Biosynthesis|"
#query = "|Cofactor-Biosynthesis|"
#query = "|Carbohydrates-Degradation|"
query = "|Polyamine-Biosynthesis|"
instances = meta.get_class_all_instances(query)
ofile = open("/home/jo/pwy.csv", "w")
ofile.write("id" + "\t" + "name" + "\t" + "ec" + "\t" + "rea" + "\n")
for idx, pwy in enumerate(instances):
if meta[pwy] == None:
print(pwy, "Pathway does not exist")
continue
rea_list = meta[pwy]["reaction_list"]
ec_list = []
reaid_list = []
for r in rea_list:
ec = meta[r]["ec_number"]
reaid = r
if ec == None:
continue
ec_nr=len(ec)