def __get_uniprot_reactions(self):
"""
Purpose: Takes reactions in the form of 'HSAXXX HSAXXX ReactionType HSAPathway and
converts each hsaXXX id to a swissprot uniprot id. Stores results inside a set of tuples
with the form (uprotA, uprotB, reaction label).
@return: Set of 4-tuples with the form (uprotA, uprotB, reaction label, direction).
"""
if self.__verbose:
print("Converting KEGG reactions to UniProt reactions...")
reaction_set = set()
for reaction in self.kegg_reactions:
hsa1 = reaction[0]
hsa2 = reaction[1]
reaction_type = reaction[2]
if hsa1 not in self.hsa_to_uprot.keys() \
or hsa2 not in self.hsa_to_uprot.keys():
continue
else:
u_prot_1 = self.hsa_to_uprot[hsa1]
u_prot_2 = self.hsa_to_uprot[hsa2]
ppi = PPI(u_prot_1, u_prot_2, [reaction_type])
if u_prot_1 != u_prot_2:
reaction_set.add(ppi)
if self.__verbose:
print("\tReaction: {}\t{}\t{}".format(
ppi.p1, ppi.p2, ppi.get_reaction_type_string()
))
reaction_set = set([(ppi.p1, ppi.p2, ppi.get_reaction_type_string()) for ppi in reaction_set])
return reaction_set
ppi.p1 = sorted(xrefs[ppi.p1].swissprot_id, cmp=s_cmp)[0]
ppi.p2 = sorted(xrefs[ppi.p2].swissprot_id, cmp=s_cmp)[0]
for ppi in unknown_ppis:
if ppi.p1 != '-':
ppi.p1 = sorted(xrefs[ppi.p1].swissprot_id, cmp=s_cmp)[0]
if ppi.p2 != '-':
ppi.p2 = sorted(xrefs[ppi.p2].swissprot_id, cmp=s_cmp)[0]
# Filter out small samples, self interactions and interactions with missing p2/p1
ppis = filter(lambda ppi: ppi.p1 != '-' and ppi.p2 != '-', ppis)
ppis = filter(lambda ppi: ppi.p1 != ppi.p2, ppis)
ppis = [ppi.split() for ppi in ppis]
ppis = set([ppi for sl in ppis for ppi in sl])
types = [ppi.get_reaction_type_string() for ppi in ppis]
type_counts = {k:0 for k in types}
for t in types:
type_counts[t] += 1
ppis = [ppi for ppi in ppis if type_counts[ppi.get_reaction_type_string()] >= 5]
fp1 = open('tmp/hprd_training_ppi.tsv', 'w')
fp2 = open('tmp/hprd_testing_ppi.tsv', 'w')
fp3 = open('tmp/unknown_hprd_ppi.tsv', 'w')
fp1.write("uniprot_a\tuniprot_a\tlabel\n")
fp2.write("uniprot_a\tuniprot_a\tlabel\n")
fp3.write("uniprot_a\tuniprot_a\tlabel\n")
test_type = [
'phosphorylation',
'dephosphorylation'
