def run(self):
system("mkdir -p %s" % self.outdir)
clone2sams = read_clone_file(self.clone_file, True)
if os.path.isdir(self.model):
model = rcommon.get_median_model(self.model)
else:
model = pickle.load(gzip.open(self.model, "rb"))
sam2total, group2sams = read_clonesize(self.numclone_file)
len2llh = read_llh(self.lenllh, intkey=True)
clone2llh = read_llh(self.clonellh)
global_dir = self.getGlobalTempDir()
lencount_dir = os.path.join(global_dir, "sam2len2count")
system("mkdir -p %s" % lencount_dir)
for s in os.listdir(self.db_dir):
samdir = os.path.join(self.db_dir, s)
lencount_file = os.path.join(lencount_dir, s)
self.addChildTarget(GetLencount(samdir, lencount_file))
self.setFollowOnTarget(
GetLlhs(
clone2sams,
self.outdir,
model,
lencount_dir,
group2sams,
self.ingroup,
self.outgroup,
len2llh,
clone2llh,
)
)
def run(self):
model = rcommon.get_median_model(self.model_dir)
self.logToMaster("Done computing median model.\n")
lens = get_lens(self.db_dir)
self.logToMaster("Done getting lengths: %s\n" %
",".join([str(l) for l in lens]))
self.addChildTarget(GetLenLlhs(self.db_dir, lens, model, self.outfile))
def main():
clone_file = sys.argv[1]
model_dir = sys.argv[2]
db_dir = sys.argv[3]
numclone_file = sys.argv[4]
outfile = sys.argv[5]
ingroup = sys.argv[6]
outgroup = sys.argv[7]
clone2sams = read_clone_file(clone_file)
model = rcommon.get_median_model(model_dir)
sam2total, group2sams = read_clonesize(numclone_file)
aaclones_likelihood(clone2sams, model, db_dir, sam2total, group2sams,
outfile, ingroup, outgroup)
def run(self):
self.logToMaster("Setting up...\n")
if not os.path.exists(self.outdir):
system("mkdir -p %s" % self.outdir)
#global_dir = self.getGlobalTempDir()
clones = lcommon.read_list(self.clonefile)
v2seq = lcommon.read_dict(self.vfile, cap=True)
j2seq = lcommon.read_dict(self.jfile, cap=True)
d2seq = lcommon.read_dict(self.dfile, cap=True)
#get the median model
model = rcommon.get_median_model(self.modeldir)
modelfile = os.path.join(self.outdir, "recomb_median_model.pickle")
pickle.dump(model, gzip.open(modelfile, 'wb'))
self.logToMaster("Done processing the input files.\n")
for clone in clones:
items = clone.split('_')
v = items[0]
seq = items[1]
j = items[2]
vdels = []
for vdel, vdelfreq in model.v2del[v].iteritems():
if vdelfreq > 0:
vdels.append(vdel)
jdels = []
for jdel, jdelfreq in model.j2del[j].iteritems():
if jdelfreq > 0:
jdels.append(jdel)
vseq = v2seq[v]
jseq = j2seq[j]
outdir = os.path.join(self.outdir, clone)
system("mkdir -p %s" % outdir)
self.addChildTarget(GetCloneEvents(clone, seq, vseq, jseq, d2seq,
outdir, modelfile, vdels, jdels))
self.setFollowOnTarget(CloneEventsAgg(self.outdir))