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from io import StringIO
import pandas as pd
import numpy as np
import pytest
import bioframe
############# tests #####################
def test_read_table():
d = """chr1\nchr2\nchr2"""
assert bioframe.read_table(StringIO(d), schema="bed3").shape == (3, 3)
# raise a value error if any columns are filled with all NA
with pytest.raises(ValueError):
bioframe.read_table(StringIO(d), schema="bed3", schema_is_strict=True)
# fill with nans to appropriate size if schema_is_strict=False (aka the default)
d = """chr1 5 10
chr1 10 20
chr2 30 40"""
assert bioframe.read_table(StringIO(d), schema="bed3", sep="\s+").shape == (3, 3)
assert bioframe.read_table(StringIO(d), schema="bed6", sep="\s+").shape == (3, 6)
assert bioframe.read_table(StringIO(d), schema="bed12", sep="\s+").shape == (3, 12)
# bedpe has 10 columns
d = """chr1 5 10 chr2 5 10 interval1 . + -
chr1 10 20 chr1 5 10 interval2 . + -
chr2 30 40 chr2 5 10 interval3 12 + -
"""
assert bioframe.read_table(
StringIO(d), schema="bedpe", sep="\s+", schema_is_strict=True
).shape == (3, 10)
def test_read_chromsizes():
d = """chr1\nchr2\nchr2"""
with pytest.raises(ValueError):
bioframe.read_chromsizes(StringIO(d))
d = """chr1\t1\nchr3\t2\nchr2\t3\n """
chromsizes = bioframe.read_chromsizes(StringIO(d))
assert type(chromsizes) is pd.Series
assert chromsizes.name == "length"
assert list(chromsizes.index) == ["chr1", "chr2", "chr3"]
assert list(chromsizes.values) == [1, 3, 2]
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