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))
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)
self.logToMaster("Done processing the input files.\n")
for clone in clones:
items = clone.split('_')
v = items[0]
seq = items[1]
j = items[2]
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))