def test_init():
block = WiggleBlock(is_fixed=True, chrom="chr")
assert block.base == 1
assert block.is_fixed == True
assert block.chrom == "chr"
assert block.start == None
assert block.step == None
assert block.span == 1
assert block._end == None
assert block.data == []
assert block._regions == []
def test_stringify_to_bedgraph(tmp_path):
block = WiggleBlock(is_fixed=True, chrom="chr", start=1, step=1)
block.take("1.1\n")
block.take("2.1\n")
block.take("3.1\n")
block.take("4.1\n")
block.take("5.1\n")
expected = """\
chr 1 1 1.1
chr 2 2 2.1
chr 3 3 3.1
chr 4 4 4.1
chr 5 5 5.1
"""
assert block._stringify_to_bedgraph() == expected
outfile = tmp_path / 'test_wiggle_block_stringify_to_bedgraph.wig'
with open(outfile, 'w') as fout:
assert block.stringify(fmt='bedgraph', writer=fout) == ""
assert outfile.read_text() == expected
def test_end():
block = WiggleBlock(is_fixed=True, chrom="chr")
block._end = 10
assert block.end == 10
block2 = WiggleBlock(is_fixed=True, chrom="chr", start=1, step=1)
block2.data = [1.1, 2.1]
assert block2.end == 2
def test_regions():
block = WiggleBlock(is_fixed=True, chrom="chr")
block._regions = [1]
assert block.regions == [1]
block2 = WiggleBlock(is_fixed=True, chrom="chr", start=1, step=1)
block2.data = [1.1, 2.1]
assert block2.regions == [1, 2]
def test_stringify_to_wiggle(tmp_path):
block = WiggleBlock(is_fixed=True, chrom="chr", start=1, step=1)
block.take("1.1\n")
block.take("2.1\n")
block.take("3.1\n")
block.take("4.1\n")
block.take("5.1\n")
expected = """\
fixedStep chrom=chr span=1 start=1 step=1
1.1
2.1
3.1
4.1
5.1
"""
assert block._stringify_to_wiggle() == expected
outfile = tmp_path / 'test_wiggle_block_stringify_to_wiggle.wig'
with open(outfile, 'w') as fout:
assert block._stringify_to_wiggle(writer=fout) == ""
assert outfile.read_text() == expected
block2 = WiggleBlock(is_fixed=False, chrom="chr")
block2.take("1\t1.1\n")
block2.take("2\t2.1\n")
block2.take("3\t3.1\n")
block2.take("4\t4.1\n")
block2.take("5\t5.1\n")
expected2 = """\
variableStep chrom=chr span=1
1 1.1
2 2.1
3 3.1
4 4.1
5 5.1
"""
assert block2._stringify_to_wiggle() == expected2
outfile2 = tmp_path / 'test_wiggle_block_stringify_to_wiggle2.wig'
with open(outfile2, 'w') as fout2:
assert block2.stringify(fmt='wiggle', writer=fout2) == ""
assert outfile2.read_text() == expected2
def test_take():
block = WiggleBlock(is_fixed=True, chrom="chr", start=1, step=1)
block.take("1.1\n")
block.take("2.1\n")
assert block.data == [1.1, 2.1]
assert block.regions == [1,2]
assert block.end == 2
with pytest.raises(WiggleInvalidDataLine):
block.take("1\t2\n")
block2 = WiggleBlock(is_fixed=False, chrom="chr")
block2.take("10\t1.1\n")
block2.take("20\t2.1\n")
assert block2.data == [1.1, 2.1]
assert block2.regions == [10, 20]
assert block2.end == 20
assert block2.start == 10
with pytest.raises(WiggleInvalidDataLine):
block2.take("3.1\n")
def test_block_id():
block = WiggleBlock(is_fixed=True, chrom="chr", start=1, step=1)
assert block.block_id == "chr:1"
def test_stats():
block = WiggleBlock(is_fixed=True, chrom="chr",
start=1, step=2, span=2)
block.take("1.1\n") # 1, 2
block.take("2.1\n") # 3, 4
block.take("3.1\n") # 5, 6
block.take("4.1\n") # 7, 8
block.take("5.1\n") # 9, 10
assert block.stats() == dict(
min=1.1,
max=5.1,
mean=3.1,
median=3.1,
sum=15.5,
count=5,
bp=10
)
block.take("6.1\n")
assert pytest.approx(block.stats("median")["median"]) == 3.6
def test_subset():
block = WiggleBlock(is_fixed=True, chrom="chr",
start=1, step=2, span=2)
block.take("1.1\n") # 1, 2
block.take("2.1\n") # 3, 4
block.take("3.1\n") # 5, 6
block.take("4.1\n") # 7, 8
block.take("5.1\n") # 9, 10
ssblock = block.subset(("chr", 2, 4))
assert ssblock.regions == [2, 3]
assert ssblock.data == [.55, 2.1]
ssblock2 = block.subset(("chr", 2, 4), partial="whole")
assert ssblock2.regions == [2, 3]
assert ssblock2.data == [1.1, 2.1]
ssblock3 = block.subset(("chr", 1, 4), qbase=0)
assert ssblock3.regions == [2, 3]
assert ssblock3.data == [.55, 2.1]
ssblock4 = block.subset(("chr", 1, 4), qbase=0, partial="whole")
assert ssblock4.regions == [2, 3]
assert ssblock4.data == [1.1, 2.1]
ssblock5 = block.subset(("chr", 1, 10))
assert ssblock5.regions == [1, 3, 5, 7, 9]
assert ssblock5.data == [1.1, 2.1, 3.1, 4.1, 5.1]
def test_stringify_error():
block = WiggleBlock(is_fixed=True, chrom="chr", start=1, step=1)
block.take("1.1\n")
with pytest.raises(WiggleUnsupportedStringifyFormat):
block.stringify(fmt="xyz")