def main():
(elutionF, geneNameF, outPrefix) = sys.argv[1:]
geneNameFH = open(geneNameF)
geneName= {}
species = {}
for line in geneNameFH:
line = line.rstrip()
ida, idb, spec = line.split("\t")
if ida not in geneName: geneName[ida] = set([])
geneName[ida].add(idb)
species[ida] = spec
species[idb] = spec
geneNameFH.close()
elutionData, scoreCalc = calcS.loadEData(elutionF)
preds = scoreCalc.getAllPairs()
out = {}
for protA, protB, _ in preds:
if protA not in species or protB not in species: continue
if species[protA] != species[protB]: continue
if species[protA] not in out: out[species[protA]] = set()
out[species[protA]].add("\t".join(sorted([protA, protB])))
for species in out:
outFH = open("%s.%s.topred.txt" % (outPrefix, species) , "w")
print >> outFH, "ProtA\tProtB"
print >> outFH, "\n".join(out[species])
outFH.close()
def main(): (elutionF, outF) = sys.argv[1:] elutionData, scoreCalc = calcS.loadEData(elutionF) scoreCalc.calculateAllPairs([calcS.MutualInformation(2)]) outFH = open(outF, "w") outFH.write(scoreCalc.toTable(False)) outFH.close()
