def __init__(self,
bedfile: str,
spacing: int = 20,
mindata: int = 50,
maxpool: int = None,
lines: list = None):
# spacing should be >= 0
if not type(spacing) == int or spacing < 0:
print("ROI: Invalid spacing: {0}; defaulting to 0".format(spacing))
spacing = 0
# mindata should be > 0
if not type(mindata) == int or mindata <= 0:
print("ROI: Invalid mindata: {0}; defaulting to 1".format(mindata))
mindata = 1
print("Loading .bed data.")
if maxpool:
print("ROI limited to max number of pools = {0}".format(maxpool))
self.source = bedfile
if lines is None:
bed_file = BedFileLoader(bedfile)
lines = bed_file.expand_columns()
self.amplicons = self.load_amplicons(lines, maxpool, -1)
if self.amplicons:
self.targets = self.define_targets(spacing, mindata)
else:
return
def __init__(self, filename: str):
bed_file = BedFileLoader(filename)
print('Loading coverage data from {}'.format(filename))
# noinspection PyProtectedMember
if bed_file.file_type != bed_file._BedFileLoader__amplicon_cov:
print('{} is not a valid amplicon_coverage file'.format(filename))
sys.exit(1)
self.targets, self.counters = self.define_targets(
bed_file.expand_columns(), bed_file.columns)
def test_len_columns_for_amplicon_cov():
bed_file = BedFileLoader(mock_dir_path + 'amplicon_cov.tsv')
expanded = bed_file.expand_columns()
assert len(bed_file.columns) == len(expanded[0])
def test_len_columns_for_effective_regions():
bed_file = BedFileLoader(mock_dir_path + 'effective_regions.bed')
expanded = bed_file.expand_columns()
assert len(bed_file.columns) == len(expanded[0])
def test_len_columns_for_general_bed():
bed_file = BedFileLoader(mock_dir_path + 'general.bed')
expanded = bed_file.expand_columns()
assert len(bed_file.columns) == len(expanded[0])
def test_len_columns_for_ampliseq_exome():
bed_file = BedFileLoader(mock_dir_path + 'ampliseq_exome.bed')
expanded = bed_file.expand_columns()
assert len(bed_file.columns) == len(expanded[0])