1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
|
import numpy as np
import pyranges as pr
from tests.helpers import assert_df_equal
a = '''Chromosome Start End Strand
chr1 6 12 +
chr1 10 20 +
chr1 22 27 -
chr1 24 30 -'''
b = '''Chromosome Start End Strand
chr1 12 32 +
chr1 14 30 +'''
c = '''Chromosome Start End Strand
chr1 8 15 +
chr1 713800 714800 -
chr1 32 34 -'''
grs = {n: pr.from_string(s) for n, s in zip(["a", "b", "c"], [a, b, c])}
unstranded_grs = {n: gr.unstrand() for n, gr in grs.items()}
features = pr.PyRanges(chromosomes=["chr1"] * 4,
starts=[0, 10, 20, 30],
ends=[10, 20, 30, 40],
strands = ["+","+","+","-"])
unstranded_features = features.unstrand()
def test_strand_vs_strand_same():
expected_result = pr.from_string("""Chromosome Start End Strand a b c
chr1 0 10 + 1 0 1
chr1 10 20 + 2 2 1
chr1 20 30 + 0 2 0
chr1 30 40 - 0 0 1""")
res = pr.count_overlaps(grs, features, strandedness="same")
res = res.apply(lambda df: df.astype({"a": np.int64, "b": np.int64, "c": np.int64}))
res.print(merge_position=True)
assert_df_equal(res.df, expected_result.df)
# def test_strand_vs_strand_opposite():
# expected_result = pr.from_string("""Chromosome Start End Strand a b c
# chr1 0 10 + 1 0 1
# chr1 10 20 + 1 2 1
# chr1 20 30 + 0 2 0
# chr1 30 40 - 0 0 1""")
# res = pr.count_overlaps(grs, features, strandedness="opposite")
# print("features")
# print(features)
# for name, gr in grs.items():
# print(name)
# print(gr)
# res.print(merge_position=True)
# assert_df_equal(res.df, expected_result.df)
|
