#!/usr/bin/env python# Denes Turei 2019# turei.denes@gmail.com# searching 2 step feedback loop motives in OmniPath# using the web service dataimporturllib.request# note, this is the core PPI network# the fully literature curated "OmniPath sensu stricto"# it is possible to query the enzyme-substrate or the# transcriptional regulation datasets too:# url = (# 'http://omnipathdb.org/interactions?# 'datasets=omnipath,kinaseextra,tfregulons,mirnatarget'# )url='http://omnipathdb.org/interactions'records=[tuple(l.decode('ascii').strip().split('\t'))forlinurllib.request.urlopen(url).readlines()][1:]stimulation={(rec[0],rec[1])forrecinrecordsifrec[3]=='1'}inhibition={(rec[0],rec[1])forrecinrecordsifrec[4]=='1'}stimulation_rev={tuple(reversed(s))forsinstimulation}inhibition_rev={tuple(reversed(i))foriininhibition}dual_negative=((stimulation&inhibition_rev)|(inhibition&stimulation_rev))dual_positive_1=stimulation&stimulation_revdual_positive_2=inhibition&inhibition_revlen(dual_negative)# 426len(dual_positive_1)# 818len(dual_positive_2)# 154
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