def checkRefOverlap(sample_copy, ref_copy, sample_frame):
sample_copy_py, ref_copy_py = PyRanges(sample_copy), PyRanges(ref_copy)
sample_copy_py.Length, ref_copy_py.Length_b = sample_copy_py.lengths(
), ref_copy_py.lengths()
overlap = sample_copy_py.join(ref_copy_py)
#overlap = PyRanges(sample_copy).join(PyRanges(ref_copy))
#print(overlap.head())
overlap_frame = reciprocal_overlap(overlap)
if overlap_frame.empty:
filtered_sample_frame = sample_frame
else:
common = sample_copy.merge(overlap_frame, on=['ID'])
filtered_sample_frame = sample_frame[(
~sample_frame.ID.isin(common.ID))]
return filtered_sample_frame
def checkParentsOverlap(sample_copy, parent_copy, filtered_sample_frame, args,
inheritance):
if args.type == 'singleton' or (
args.type == 'duo' and inheritance == 'Found_in_Father'
and args.mother_duo) or (args.type == 'duo'
and inheritance == 'Found_in_Mother'
and args.father_duo):
# Initialize columns and set to -1 if parents file not provided
filtered_sample_frame[inheritance] = 'None'
return filtered_sample_frame
colnames = [
'CHROM', 'POS', 'ID', 'REF', "ALT_1", 'ALT_2', "ALT_3", "QUAL",
'FILTER_PASS', "END", "SVLEN"
]
sample_copy_py, parent_copy_py = PyRanges(sample_copy), PyRanges(
parent_copy)
sample_copy_py.Length, parent_copy_py.Length_b, = sample_copy_py.lengths(
), parent_copy_py.lengths()
overlap_sample_parent = sample_copy_py.join(parent_copy_py)
denovo_parent_frame = reciprocal_overlap(overlap_sample_parent)[colnames]
if denovo_parent_frame.empty:
filtered_sample_frame[inheritance] = 'False'
else:
parent_filtered_sample_frame = pd.merge(filtered_sample_frame,
denovo_parent_frame,
on=None,
how='left',
indicator=inheritance)
parent_filtered_sample_frame[inheritance] = np.where(
parent_filtered_sample_frame[inheritance] == 'both', 'True',
'False')
filtered_sample_frame = parent_filtered_sample_frame.drop_duplicates(
).reset_index(drop=True)
return filtered_sample_frame