def quantitate_expression_noparallel(samples, run_parallel):
"""
run transcript quantitation for algorithms that don't run in parallel
"""
data = samples[0][0]
if "express" in dd.get_expression_caller(data):
samples = run_parallel("run_express", samples)
samples = run_parallel("run_dexseq", samples)
if "rmats" in dd.get_splicecaller(data):
samples = run_parallel("run_rmats", samples)
return samples
def splicecall_prepare(data, run_parallel):
"""Entry point for doing alternative splice callers"""
gtf_file = dd.get_gtf_file(data)
caller_fns = get_callers()
to_process = []
caller = "rmats"
for sample in data:
if dd.get_replicate(sample[0]) == 1:
mimic = copy.copy(sample[0])
if caller in dd.get_splicecaller(sample[0]):
if caller in caller_fns and dd.get_phenotype(mimic) != "control":
mimic["rmats_fn"] = caller
name = dd.get_sample_name(mimic)
rep_mimic = _get_replicate_samples(mimic, data)
mimic = _get_paired_samples(mimic, data)
if mimic:
to_process.append(mimic)
else:
logger.info("Skipping alternative splice calling. No input sample for %s" % name)
if to_process:
after_process = run_parallel("splicecalling", to_process)
data = _sync(data, after_process)
return data
def run_rmats(data):
"""Detect differential alternative splicing by rMATS"""
splicecaller = dd.get_splicecaller(data)
if "rmats" in splicecaller:
data = splice.peakcall_prepare(data)
return [[data]]
def _get_splice_file(x, fn_name):
"""Get peak caller for this file name."""
for caller in dd.get_splicecaller(x):
if fn_name.find(caller) > -1:
return caller
return os.path.basename(fn_name)