options.neighbor,
localproteinfile,
mapProtNamesToMasterIdx,
localkeyfile,
)
mvote.writeCoveredLabels(coveredLabels, options.coveredlabels)
#### Phase 3: Write Output
parts = options.outfile.split("/")
name = parts[-1]
if len(parts) > 1:
path = "/".join(parts[:-1])
else:
path = "."
if options.mode == 0:
name = "OrdMV" + name
outfilename = "/".join([path, name])
elif options.mode == 1:
name = "DSDUnweight" + name
outfilename = "/".join([path, name])
elif options.mode == 2:
name = "DSDWeighted" + name
outfilename = "/".join([path, name])
elif options.mode == 3:
name = "DSDWeightedIterative" + name
outfilename = "/".join([path, name])
mvote.writeOutput(masterPredictionMatrix, outfilename)
#### print ppfDSD[1,3], ppfDSD[5,11]
#### Phase 2: Conduct Majority Voting
if options.mode == 0:
prediction = mvote.ordinaryMV(ppbAdj, ppbLabel, pnFoldIndex, pnRD)
elif options.neighbor <= 0 or options.neighbor >= N / 2:
options.neighbor == 10
print >>sys.stderr, "the setting for top DSD neighbors is invalid,"
print >>sys.stderr, "change to 10 instead by default.\n"
if options.mode == 1:
prediction = mvote.DSDUnweightMV(ppfDSD, ppbLabel, pnFoldIndex, pnRD, options.neighbor)
elif options.mode == 2:
prediction = mvote.DSDWeightedMV(ppfDSD, ppbLabel, pnFoldIndex, pnRD, options.neighbor)
elif options.mode == 3:
prediction = mvote.SeqDSDWeightedMV(
ppfDSD, ppfSeq, ppbLabel, pnFoldIndex, pnRD, options.neighbor, options.a, options.b, options.N
)
#### Phase 3: Write Output
if options.mode == 0:
options.outfile = "OrdMV" + options.outfile
elif options.mode == 1:
options.outfile = "DSDUnweight" + options.outfile
elif options.mode == 2:
options.outfile = "DSDWeighted" + options.outfile
elif options.mode == 3:
options.outfile = "SequenceDSD" + options.outfile
mvote.writeOutput(prediction, options.outfile)
