def check_track_clone_options(parser, options):
options.clones = None
if options.clonefile:
libcommon.check_options_file(options.clonefile)
options.clones = libcommon.read_list(options.clonefile)
if options.track_minfreq > 1.0:
parser.error("--track_minfreq is the proportion, not %, should be < 1")
def run(self):
db_dir = self.args[0]
sam_file = self.args[1]
minsam = int(self.args[2])
outdir = self.args[3]
if not os.path.exists(outdir):
system("mkdir -p %s" % outdir)
samples = lcommon.read_list(sam_file)
c2s_dir = self.c2s_dir
if c2s_dir is None:
global_dir = self.getGlobalTempDir()
c2s_dir = os.path.join(global_dir, "clone2sam2size_dir")
system("mkdir -p %s" % c2s_dir)
sizetype = 'freq'
self.addChildTarget(scommon.GetClone2Samples(db_dir, c2s_dir,
sizetype, samples))
self.setFollowOnTarget(OverlapClones(db_dir, c2s_dir, minsam,
self.maxsam, samples, 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)
#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))