chip = pd.read_table(chip_f,
sep="\t",
usecols=[0, 1, 2, 5],
header=None,
names="Chromosome Start End Strand".split())
cgr = PyRanges(chip, copy_df=False)
background = pd.read_table(background_f,
sep="\t",
usecols=[0, 1, 2, 5],
header=None,
names="Chromosome Start End Strand".split())
bgr = PyRanges(background, copy_df=False)
start = time()
result = cgr.intersection(bgr, strandedness="same")
end = time()
print(result)
total = end - start
total_dt = datetime.datetime.fromtimestamp(total)
minutes_seconds = total_dt.strftime('%-M.%-S.%f')
open(snakemake.output[0], "w+").write(minutes_seconds)
print("first range finished")
end = time()
b_gr = PyRanges(b)
print("second range finished")
end2 = time()
first = datetime.datetime.fromtimestamp(end - start).strftime('%M\t%S\n')
second = datetime.datetime.fromtimestamp(end2 - end).strftime('%M\t%S\n')
start_overlap = time()
o_gr = c_gr.intersection(b_gr)
end_overlap = time()
overlap_time = datetime.datetime.fromtimestamp(end_overlap - start_overlap).strftime('%M\t%S\n')
print(first, second, overlap_time, sep="\n")
print(o_gr)
# all reads:
# 05 26
# +--------------+----------+----------+----------+
# | Chromosome | Start | End | Strand |
# |--------------+----------+----------+----------|