def test_bw():
b = BigWig("libBigWig/test/test.bw")
assert repr(b) == "BigWig('libBigWig/test/test.bw')"
intervals = list(b("1", 0, 99))
assert intervals[0] == Interval(chrom='1', start=0, end=1, value=0.10000000149011612)
assert intervals[1] == Interval(chrom='1', start=1, end=2, value=0.20000000298023224)
assert intervals[2] == Interval(chrom='1', start=2, end=3, value=0.30000001192092896)
# default is to include all values
vals = b.values("1", 0, 9)
exp = array('f', [0.10000000149011612, 0.20000000298023224, 0.30000001192092896, nan, nan, nan, nan, nan, nan])
arr_equal(vals, exp)
vals = b.values("1", 0, 9, False)
exp = array('f', [0.10000000149011612, 0.20000000298023224, 0.30000001192092896])
arr_equal(vals, exp)
v = b.stats("1", 0, 9)
assert v == 0.2000000054637591
v = b.stats("1", 0, 9, stat="stdev")
assert v == 0.10000000521540645
v = b.stats("1", 0, 4, stat="coverage")
assert v == 0.75
v = b.stats("1", 0, 4, stat="coverage", nBins=2)
assert v == array('d', [1.0, 0.5])
b.close()
def read_gerp(region, sends, path='/scratch/ucgd/lustre/u1021864/serial/hg19.gerp.bw'):
gerp = BigWig(path)
exongerp=[]
chrom, se = region.split(":")
s, e = map(int, se.split("-"))
if not chrom.startswith("chr"):
chrom = "chr" + chrom
for key in sends:
for (exs, exe) in zip(sends[key][0], sends[key][1]):
exongerp.extend(np.frombuffer(gerp.values(chrom, int(exs)-1, int(exe)), dtype='f'))
return np.frombuffer(gerp.values(chrom, int(s)-1, int(e)), dtype='f'), exongerp
def test_bw():
b = BigWig("libBigWig/test/test.bw")
assert repr(b) == "BigWig('libBigWig/test/test.bw')"
intervals = list(b("1", 0, 99))
assert intervals[0] == Interval(chrom='1',
start=0,
end=1,
value=0.10000000149011612)
assert intervals[1] == Interval(chrom='1',
start=1,
end=2,
value=0.20000000298023224)
assert intervals[2] == Interval(chrom='1',
start=2,
end=3,
value=0.30000001192092896)
# default is to include all values
vals = b.values("1", 0, 9)
exp = array('f', [
0.10000000149011612, 0.20000000298023224, 0.30000001192092896, nan,
nan, nan, nan, nan, nan
])
arr_equal(vals, exp)
vals = b.values("1", 0, 9, False)
exp = array(
'f', [0.10000000149011612, 0.20000000298023224, 0.30000001192092896])
arr_equal(vals, exp)
v = b.stats("1", 0, 9)
assert v == 0.2000000054637591
v = b.stats("1", 0, 9, stat="stdev")
assert v == 0.10000000521540645
v = b.stats("1", 0, 4, stat="coverage")
assert v == 0.75
v = b.stats("1", 0, 4, stat="coverage", nBins=2)
assert v == array('d', [1.0, 0.5])
b.close()
def test_bad_chr():
b = BigWig("libBigWig/test/test.bw")
assert b.stats("chr1", 0, 10) is None
v = b.values("chr1", 0, 10)
assert len(v) == 0, v
def test_bad_chr():
b = BigWig("libBigWig/test/test.bw")
assert b.stats("chr1", 0, 10) is None
v = b.values("chr1", 0, 10)
assert len(v) == 0, v
