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import sys
from io import StringIO
import pandas as pd
import pytest
import bioframe
is_big_endian = sys.byteorder == "big"
############# 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=r"\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 isinstance(chromsizes, pd.Series)
assert chromsizes.name == "length"
assert list(chromsizes.index) == ["chr1", "chr2", "chr3"]
assert list(chromsizes.values) == [1, 3, 2]
def test_read_beds():
# Checking that we properly read common bed schemas
schemas = ['narrowPeak', 'jaspar', 'bed9', 'bed12']
for schema in schemas:
_ = bioframe.read_table(f'tests/test_data/{schema}.bed', schema=schema,
schema_is_strict=True)
@pytest.mark.skipif(is_big_endian, reason="Test skipped on big-endian systems")
def test_read_sam():
pytest.importorskip("pysam")
# SAM file taken from https://github.com/samtools/samtools/blob/develop/examples/toy.sam
_ = bioframe.read_alignments('tests/test_data/toy.sam')
@pytest.mark.skipif(is_big_endian, reason="Test skipped on big-endian systems")
def test_read_bam():
pytest.importorskip("pysam")
# converted toy.sam via `samtools view -bS toy.sam > toy.bam;
# index file created with `samtools index toy.bam`
_ = bioframe.read_alignments('tests/test_data/toy.bam')
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