def make_window_regions(configuration):
print("{0} Creating window regions...".format(INFO))
print("{0} Processing type is: {1}".format(INFO, configuration['processing']['type']))
if configuration['processing']['type'] == 'multi':
from parallel import par_make_window_regions
return par_make_window_regions(configuration=configuration)
windowsize = configuration["window_size"]
chromosome = configuration["chromosome"]
print("{0} Window size: {1}".format(INFO, windowsize))
print("{0} Chromosome: {1}".format(INFO, chromosome))
regions = configuration["regions"]
print("{0} Regions used {1}".format(INFO, regions))
regions_list = [(start, end) for start, end
in zip(regions["start"], regions["end"])]
regions_created = []
counter = 0
for r in regions_list:
start_idx = r[0]
end_idx = r[1]
print("{0} Start index: {1}".format(INFO, start_idx))
sys.stdout.flush()
print("{0} End index: {1}".format(INFO, end_idx))
sys.stdout.flush()
region = Region(idx=counter,
start=start_idx,
end=end_idx,
window_size=windowsize)
kwargs = {"sam_read_config": configuration["sam_read_config"]}
if "debug" in configuration:
kwargs["debug"] = configuration["debug"]
print("{0} Creating WGA Windows...".format(INFO))
sys.stdout.flush()
region.make_wga_windows(chromosome=chromosome,
ref_filename=configuration["reference_file"]["filename"],
bam_filename=configuration["wga_file"]["filename"],
**kwargs)
if region.get_n_windows(type_=WindowType.WGA) == 0:
raise Error("WGA windows have not been created")
else:
print("{0} Number of WGA "
"windows: {1}".format(INFO,
region.get_n_windows(type_=WindowType.WGA)))
sys.stdout.flush()
print("{0} Creating No WGA Windows...".format(INFO))
sys.stdout.flush()
region.make_no_wga_windows(chromosome=chromosome,
ref_filename=configuration["reference_file"]["filename"],
bam_filename=configuration["no_wga_file"]["filename"],
**kwargs)
if region.get_n_windows(type_=WindowType.NO_WGA) == 0:
raise Error("Non-WGA windows have not been created")
else:
print("{0} Number of Non WGA"
" windows: {1}".format(INFO,
region.get_n_windows(type_=WindowType.NO_WGA)))
sys.stdout.flush()
regions_created.append(region)
counter += 1
return regions_created
def make_window_regions(configuration):
print("{0} Creating window regions...".format(INFO))
windowsize = configuration["window_size"]
chromosome = configuration["chromosome"]
print("{0} Window size: {1}".format(INFO, windowsize))
print("{0} Chromosome: {1}".format(INFO, chromosome))
regions = configuration["regions"]
print("{0} Regions used {1}".format(INFO, regions))
regions_list = [(start, end)
for start, end in zip(regions["start"], regions["end"])]
regions_created = []
counter = 0
for r in regions_list:
start_idx = r[0]
end_idx = r[1]
print("{0} Start index: {1}".format(INFO, start_idx))
print("{0} End index: {1}".format(INFO, end_idx))
region = Region(idx=counter,
start=start_idx,
end=end_idx,
window_size=windowsize)
kwargs = {}
if "quality_theshold" in configuration:
kwargs["quality_theshold"] = configuration["quality_theshold"]
if "debug" in configuration:
kwargs["debug"] = configuration["debug"]
print("{0} Creating WGA Windows...".format(INFO))
region.make_wga_windows(
chromosome=chromosome,
ref_filename=configuration["reference_file"]["filename"],
test_filename=configuration["test_file"]["filename"],
**kwargs)
if region.get_n_windows(type_=WindowType.WGA) == 0:
raise Error("WGA windows have not been created")
else:
print("{0} Number of WGA windows: {1}".format(
INFO, region.get_n_windows(type_=WindowType.WGA)))
print("{0} Creating No WGA Windows...".format(INFO))
region.make_no_wga_windows(
chromosome=chromosome,
ref_filename=configuration["reference_file"]["filename"],
test_filename=configuration["no_wga_file"]["filename"],
**kwargs)
if region.get_n_windows(type_=WindowType.NO_WGA) == 0:
raise Error("Non-WGA windows have not been created")
else:
print("{0} Number of non-wga"
" windows: {1}".format(
INFO, region.get_n_windows(type_=WindowType.NO_WGA)))
if "check_windowing_sanity" in configuration and \
configuration["check_windowing_sanity"]:
region.check_windows_sanity()
# compute the mixed windows for the region
region.get_mixed_windows()
# filter the windows for N's
if "remove_windows_with_N" in configuration and\
configuration["remove_windows_with_N"]:
print("{0} Filtering windows for Ns...".format(INFO))
region.remove_windows_with_ns()
print("{0} Number of wga windows"
" after filtering: {1}".format(
INFO, region.get_n_windows(type_=WindowType.WGA)))
print("{0} Number of non-wga windows"
" after filtering: {1}".format(
INFO, region.get_n_windows(type_=WindowType.NO_WGA)))
print("{0} Done...".format(INFO))
elif "mark_N_windows" in configuration and\
configuration["mark_N_windows"]:
print("{0} Marking N "
" windows with: {1}".format(
INFO, configuration["mark_for_N_windows"]))
counter_ns = \
region.mark_windows_with_ns(n_mark=configuration["mark_for_N_windows"])
print("{0} Marked as N {1} Windows".format(INFO, counter_ns))
else:
print("{0} No filtering windows"
" for Ns requested...".format(INFO))
print("{0} Number of mixed "
"windows: {1}".format(INFO, region.get_n_mixed_windows()))
print("{0} Number of N windows: {1}".format(INFO,
region.count_n_windows()))
if "outlier_remove" in configuration and\
configuration["outlier_remove"]:
region.remove_outliers(configuration=configuration)
print("{0} Number of windows "
"after outlier removal: {1}".format(
INFO, region.get_n_mixed_windows()))
print("{0} Number of N windows "
"after outlier removal {1}".format(INFO,
region.count_n_windows()))
else:
print("{0} No outlier " "removal performed".format(INFO))
# save the region statistics
region.save_mixed_windows_statistic(statistic="mean")
regions_created.append(region)
counter += 1
return regions_created