def regions_worker(worker_id, configuration, regions_chuncks, regions_dict,
msg_dict, errors_dict):
try:
args = {}
if "debug" in configuration:
args["debug"] = configuration["debug"]
args["sam_read_config"] = configuration["sam_read_config"]
windowsize = configuration["window_size"]
chromosome = configuration["chromosome"]
ref_filename = configuration["reference_file"]['filename']
tstart = time.perf_counter()
for rid in regions_chuncks.keys():
worker_chunck = regions_chuncks[rid][worker_id]
args["start_idx"] = worker_chunck[0]
args["end_idx"] = worker_chunck[1]
args["windowsize"] = windowsize
wga_windows = []
no_wga_windows = []
bam_filename = configuration['wga_file']['filename']
wga_windows = extract_windows(chromosome=chromosome,
ref_filename=ref_filename,
bam_filename=bam_filename,
**args)
bam_filename = configuration['no_wga_file']['filename']
no_wga_windows = extract_windows(chromosome=chromosome,
ref_filename=ref_filename,
bam_filename=bam_filename,
**args)
regions_dict[rid][worker_id] = {
"wga_windows": wga_windows,
"no_wga_windows": no_wga_windows
}
tend = time.perf_counter()
msg = ("Process {0} finished in {1} secs").format(
worker_id, tend - tstart)
msg_dict[worker_id] = msg
except Exception as e:
msg = "An exception occured in worker {0}. Exception message {1}".format(
worker_id, str(e))
errors_dict[worker_id] = msg
return
def make_no_wga_windows(self, chromosome, ref_filename, test_filename,
**kwargs):
args = {
"start_idx": self._start,
"end_idx": self._end,
"windowsize": self._w_size
}
if "quality_theshold" in kwargs:
args["quality_theshold"] = kwargs["quality_theshold"]
if "debug" in kwargs:
args["debug"] = kwargs["debug"]
windows = extract_windows(chromosome=chromosome,
ref_filename=ref_filename,
test_filename=test_filename,
**args)
print("{0} Start Window: Start/End idx {1}".format(
INFO, windows[0].get_start_end_pos()))
print("{0} End Window: Start/End idx {1}".format(
INFO, windows[-1].get_start_end_pos()))
self._windows[WindowType.NO_WGA] = windows
def make_no_wga_windows(self, chromosome,
ref_filename,
bam_filename, **kwargs):
args = {"start_idx": self._start,
"end_idx": self._end,
"windowsize": self._w_size}
if "debug" in kwargs:
args["debug"] = kwargs["debug"]
args["sam_read_config"] = kwargs["sam_read_config"]
windows = extract_windows(chromosome=chromosome,
ref_filename=ref_filename,
bam_filename=bam_filename,
**args)
print("{0} Region Start Window "
"Coords: Start/End idx {1}".format(INFO, windows[0].start_end_pos))
print("{0} Region End Window "
"Coords: Start/End idx {1}".format(INFO, windows[-1].start_end_pos))
self._windows[WindowType.NO_WGA] = windows