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Granularize api tests #47

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Jun 30, 2024
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Granularize api tests #47

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109 changes: 62 additions & 47 deletions pybigtools/tests/test_api.py
View file
Original file line number Diff line number Diff line change
@@ -151,6 +151,12 @@ def test_records(bw, bb):
assert len(list(bw.records("chr17", 100_000, 110_000))) == 1515
assert len(list(bb.records("chr21", 10_000_000, 20_000_000))) == 233

# Unknown chrom => exception
assert pytest.raises(KeyError, bw.records, "chr11")
assert pytest.raises(KeyError, bb.records, "chr11")


def test_records_oob(bw, bb):
# Out of bounds start/end are truncated
x = list(bw.records("chr17", 0, 100_000))
assert len(x) == 8641
@@ -175,10 +181,6 @@ def test_records(bw, bb):
assert len(list(bb.records("chr21", -1000, -500))) == 0
assert len(list(bb.records("chr21", 48_129_895, 49_000_000))) == 0

# Unknown chrom => exception
assert pytest.raises(KeyError, bw.records, "chr11")
assert pytest.raises(KeyError, bb.records, "chr11")


def test_zoom_records(bw, bb):
# (chrom, None, None) => all records on chrom
@@ -193,27 +195,6 @@ def test_zoom_records(bw, bb):
assert len(list(bw.zoom_records(10, "chr17", 100_000, 110_000))) == 766
assert len(list(bb.zoom_records(3911, "chr21", 10_000_000, 20_000_000))) == 154

# Out of bounds start/end are truncated
x = list(bw.zoom_records(10, "chr17", 0, 100_000))
assert len(x) == 2940
assert list(bw.zoom_records(10, "chr17", -1000, 100_000)) == x
x = list(bb.zoom_records(3911, "chr21", 0, 10_000_000))
assert len(x) == 6
assert list(bb.zoom_records(3911, "chr21", -1000, 10_000_000)) == x

y = list(bw.zoom_records(10, "chr17", 0, bw.chroms("chr17")))
assert len(y) == 13811
assert list(bw.zoom_records(10, "chr17", 0, bw.chroms("chr17") * 2)) == y
y = list(bb.zoom_records(3911, "chr21", 0, bb.chroms("chr21")))
assert len(y) == 1676
assert list(bb.zoom_records(3911, "chr21", 0, bb.chroms("chr21") * 2)) == y

# Fully out of bounds ranges return no records
assert len(list(bw.zoom_records(10, "chr17", -1000, -500))) == 0
assert len(list(bw.zoom_records(10, "chr17", 83_257_441, 84_000_000))) == 0
assert len(list(bb.zoom_records(3911, "chr21", -1000, -500))) == 0
assert len(list(bb.zoom_records(3911, "chr21", 48_129_895, 49_000_000))) == 0

assert next(bw.zoom_records(10, "chr17", 0, 100_000)) == (
59898,
59908,
@@ -226,7 +207,7 @@ def test_zoom_records(bw, bb):
"sum_squares": 0.2303919643163681,
},
)
assert next(bw.zoom_records(160, "chr17", 0, 100000)) == (
assert next(bw.zoom_records(160, "chr17", 0, 100_000)) == (
59898,
60058,
{
@@ -248,21 +229,46 @@ def test_zoom_records(bw, bb):
assert pytest.raises(KeyError, bb.zoom_records, 3911, "chr11")


def test_values_no_end(bw, bb):
def test_zoom_records_oob(bw, bb):
# Out of bounds start/end are truncated
x = list(bw.zoom_records(10, "chr17", 0, 100_000))
assert len(x) == 2940
assert list(bw.zoom_records(10, "chr17", -1000, 100_000)) == x
x = list(bb.zoom_records(3911, "chr21", 0, 10_000_000))
assert len(x) == 6
assert list(bb.zoom_records(3911, "chr21", -1000, 10_000_000)) == x

y = list(bw.zoom_records(10, "chr17", 0, bw.chroms("chr17")))
assert len(y) == 13811
assert list(bw.zoom_records(10, "chr17", 0, bw.chroms("chr17") * 2)) == y
y = list(bb.zoom_records(3911, "chr21", 0, bb.chroms("chr21")))
assert len(y) == 1676
assert list(bb.zoom_records(3911, "chr21", 0, bb.chroms("chr21") * 2)) == y

# Fully out of bounds ranges return no records
assert len(list(bw.zoom_records(10, "chr17", -1000, -500))) == 0
assert len(list(bw.zoom_records(10, "chr17", 83_257_441, 84_000_000))) == 0
assert len(list(bb.zoom_records(3911, "chr21", -1000, -500))) == 0
assert len(list(bb.zoom_records(3911, "chr21", 48_129_895, 49_000_000))) == 0


def test_values_bp(bw, bb):
# (chrom, None, None) => all values on chrom
assert len(bw.values("chr17")) == 83_257_441
assert len(bb.values("chr21")) == 48_129_895

# (chrom, start, None) => all values from (start, <chrom_end>)
assert len(bw.values("chr17", 0)) == 83_257_441
assert len(bw.values("chr17", 10)) == 83_257_441 - 10
assert len(bb.values("chr21", 0)) == 48_129_895
assert len(bb.values("chr21", 10)) == 48_129_895 - 10


def test_values(bw, bb):
# (chrom, start, end)
assert len(bw.values("chr17", 100_000, 110_000)) == 10_000
assert len(bb.values("chr21", 10_148_000, 10_158_000)) == 10_000


def test_values_binned(bw, bb):
assert len(bw.values("chr17", 100000, 110000, 10)) == 10
assert len(bb.values("chr21", 10_148_000, 10_158_000, 10)) == 10

@@ -275,6 +281,8 @@ def test_values(bw, bb):
assert bw.values("chr17", 100000, 110000, 10, "min")[0] == 0.05403999984264374
assert bb.values("chr21", 10_148_000, 10_158_000, 10, "min")[0] == 0.0


def test_values_binned_exact(bw, bb):
assert (
bw.values("chr17", 100000, 110000, 10, "mean", exact=True)[0]
== 0.4542629980980206
@@ -294,6 +302,8 @@ def test_values(bw, bb):
0.06791999936103821,
]


def test_values_binned_missing_oob(bw, bb):
assert list(
bw.values("chr17", 59890, 59900, 10, "mean", exact=True, missing=-1.0)
) == [
@@ -321,6 +331,29 @@ def test_values(bw, bb):
x = bb.values("chr21", -10, 10, 20, "mean", exact=True, missing=0.0, oob=0.0)
assert x[0] == 0.0


def test_values_binned_estimate_differences(bw, bb):
# Some differences in estimates between pybigtools to other libs
# Namely, bigtools calculates estimates by taking the
# sum of nanmeans over covered bases (summary.sum/summary.covered_bases)
# and dividing by covered bases (overlap between zoom and bin)
# So, including these as cases where the calculated value is different
vals = bw.values("chr17", 85525, 85730, bins=2, exact=False)
assert list(vals) == [0.15392776003070907, 2.728891665264241]
vals = bw.values("chr17", 85525, 85730, bins=2, exact=True)
assert list(vals) == [0.06770934917680595, 2.4864424403431347]
vals = bw.values("chr17", 59900, 60105, bins=2, exact=False)
assert list(vals) == [0.5358060553962108, 0.5513471488813751]
vals = bw.values("chr17", 59900, 60105, bins=2, exact=True)
assert list(vals) == [0.5362001863472602, 0.5527710799959679]

vals = bb.values("chr21", 14_760_000, 14_800_000, bins=1, exact=False)
assert list(vals) == [1.2572170068028603]
vals = bb.values("chr21", 14_760_000, 14_800_000, bins=1, exact=True)
assert list(vals) == [1.3408662900188324]


def test_values_assign_to_array(bw, bb):
# The returned array is the same as the one passed, so both show the same values
arr = np.zeros(20)
ret_arr = bw.values(
@@ -341,24 +374,6 @@ def test_values(bw, bb):
assert ret_arr[19] == 0.0
assert np.array_equal(arr, ret_arr, equal_nan=True)

# Some differences in estimates between pybigtools to other libs
# Namely, bigtools calculates estimates by taking the
# sum of nanmeans over covered bases (summary.sum/summary.covered_bases) and dividing by covered bases (overlap between zooom and bin)
# So, including these as cases where the calculated value is different
vals = bw.values("chr17", 85525, 85730, bins=2, exact=False)
assert list(vals) == [0.15392776003070907, 2.728891665264241]
vals = bw.values("chr17", 85525, 85730, bins=2, exact=True)
assert list(vals) == [0.06770934917680595, 2.4864424403431347]
vals = bw.values("chr17", 59900, 60105, bins=2, exact=False)
assert list(vals) == [0.5358060553962108, 0.5513471488813751]
vals = bw.values("chr17", 59900, 60105, bins=2, exact=True)
assert list(vals) == [0.5362001863472602, 0.5527710799959679]

vals = bb.values("chr21", 14_760_000, 14_800_000, bins=1, exact=False)
assert list(vals) == [1.2572170068028603]
vals = bb.values("chr21", 14_760_000, 14_800_000, bins=1, exact=True)
assert list(vals) == [1.3408662900188324]


def test_big_gene_pred():
bb = pybigtools.open(REPO_ROOT / "bigtools/resources/test/bigGenePred.bb")