def _maybe_add_peaks(algorithm, sample, out):
for caller in dd.get_peakcaller(sample):
out_dir = os.path.join(dd.get_work_dir(sample), caller, dd.get_sample_name(sample))
if os.path.exists(out_dir):
out.append({"path": out_dir,
"type": "directory",
"ext": caller})
return out
def peakcall_prepare(data, run_parallel):
"""Entry point for doing peak calling"""
caller_fns = get_callers()
to_process = []
for sample in data:
mimic = copy.copy(sample[0])
for caller in dd.get_peakcaller(sample[0]):
if caller in caller_fns and dd.get_phenotype(mimic) == "chip":
mimic["peak_fn"] = caller
name = dd.get_sample_name(mimic)
mimic = _get_paired_samples(mimic, data)
if mimic:
to_process.append(mimic)
else:
logger.info("Skipping peak calling. No input sample for %s" % name)
if to_process:
after_process = run_parallel("peakcalling", to_process)
data = _sync(data, after_process)
return data
def peakcall_prepare(data, run_parallel):
"""Entry point for doing peak calling"""
caller_fns = get_callers()
to_process = []
for sample in data:
mimic = copy.copy(sample[0])
for caller in dd.get_peakcaller(sample[0]):
if caller in caller_fns and dd.get_phenotype(mimic) == "chip":
mimic["peak_fn"] = caller
name = dd.get_sample_name(mimic)
mimic = _get_paired_samples(mimic, data)
if mimic:
to_process.append(mimic)
else:
logger.info(
"Skipping peak calling. No input sample for %s" % name)
if to_process:
after_process = run_parallel("peakcalling", to_process)
data = _sync(data, after_process)
return data
def peakcall_prepare(data, run_parallel):
"""Entry point for doing peak calling"""
caller_fns = get_callers()
to_process = []
for sample in data:
mimic = copy.copy(sample[0])
callers = dd.get_peakcaller(sample[0])
if not isinstance(callers, list):
callers = [callers]
for caller in callers:
if caller in caller_fns:
mimic["peak_fn"] = caller
name = dd.get_sample_name(mimic)
mimic = _check(mimic, data)
if mimic:
to_process.append(mimic)
else:
logger.info("Skipping peak calling. No input sample for %s" % name)
if to_process:
after_process = run_parallel("peakcalling", to_process)
data = _sync(data, after_process)
return data
def peakcall_prepare(data, run_parallel):
"""Entry point for doing peak calling"""
caller_fns = get_callers()
to_process = []
for sample in data:
mimic = copy.copy(sample[0])
callers = dd.get_peakcaller(sample[0])
if not isinstance(callers, list):
callers = [callers]
for caller in callers:
if caller in caller_fns:
mimic["peak_fn"] = caller
name = dd.get_sample_name(mimic)
mimic = _check(mimic, data)
if mimic:
to_process.append(mimic)
else:
logger.info("Skipping peak calling. No input sample for %s" % name)
if to_process:
after_process = run_parallel("peakcalling", to_process)
data = _sync(data, after_process)
return data
def _get_peak_file(x, fn_name):
"""Get peak caller for this file name."""
for caller in dd.get_peakcaller(x):
if fn_name.find(caller) > -1:
return caller
return os.path.basename(fn_name)
def _get_peak_file(x, fn_name):
"""Get peak caller for this file name."""
for caller in dd.get_peakcaller(x):
if fn_name.find(caller) > -1:
return caller
return os.path.basename(fn_name)