def train():
os.chdir(submitDir)
opt.mode = "train"
imm = ImmApp(opt=opt)
return imm.run()
def score():
os.chdir(submitDir)
opt.mode = "score"
imm = ImmApp(opt=opt)
return imm.run(depend=jobs)
for id in ids:
seqDb.finById(id=id)
immIdToSeqIds = dict(((id, [id]) for id in ids))
immIdToSeqIdsFile = pabs("test.immapp.seqids.pkl")
dumpObj(immIdToSeqIds, immIdToSeqIdsFile)
opt.immIdToSeqIds = immIdToSeqIdsFile
opt.mode = "train"
ImmApp.fillWithDefaultOptions(opt)
# imm = ImmApp(opt=opt)
# jobs = imm.run()
for (reduceScoresEarly, cwd) in ((1, "imm.test.red_early_1"), (0, "imm.test.red_early_0")):
immIds = ImmStore.open(path=opt.immDb, mode="r").listImmIdsWithIdScoreIdent()
immIdsFile = pabs("test.immapp.immids.pkl")
dumpObj(immIds, immIdsFile)
opt.cwd = pabs(cwd)
opt.mode = "score"
opt.reduceScoresEarly = reduceScoresEarly
opt.outDir = pabs(pjoin(opt.cwd, "score"))
opt.immIds = immIdsFile
opt.nImmBatches = 3
opt.inpSeq = pjoin(seqDbPath, "195.fasta.gz")
opt.outScoreComb = pabs(pjoin(opt.cwd, "score.comb"))
imm = ImmApp(opt=opt)
imm.run(depend=jobs)