INNER CODE UNIT · Python
read_coverage_file
cbg-ethz/V-pipe · workflow/scripts/alignmentIntervals.py:252
def read_coverage_file(input_file, reference_file, window_len, window_shift):
out_dict = {}
idx = 0
with open(input_file, "r") as infile:
for line in infile:
record = line.rstrip().split("\t")
key = record[0]
if len(record) > 1:
win_len = int(window_len[idx]) if window_len else None
win_shift = int(window_shift[idx]) if window_shift else None
reference_name, intervals = parse_region(
record[1], True, reference_file, win_len, win_shift
)
idx += 1
out_dict[key] = [reference_name, intervals]
return out_dict