def _get_multiplier(samples):
"""Get multiplier to get jobs
only for samples that have input
"""
to_process = 1.0
for sample in samples:
if dd.get_phenotype(sample[0]) != "control" and dd.get_replicate(sample[0]) == 1:
to_process += 1.0
if to_process / len(samples) < 1.0:
to_process = 1.0
else:
to_process = to_process / len(samples)
return to_process
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
