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|
import pytest
import pandas as pd
from pyranges import PyRanges
def pytest_configure(config):
config.addinivalue_line(
"markers", "bedtools: tests rely on",
)
config.addinivalue_line(
"markers", "explore: functionality not ready for prime-time"
)
@pytest.fixture
def names():
return "Chromosome Start End Name Score Strand".split()
@pytest.fixture
def chip_10(names):
df = pd.read_csv("tests/chip_10.bed", header=None, names=names, sep="\t")
gr = PyRanges(df)
assert gr.stranded
return gr
@pytest.fixture
def f1(names):
df = pd.read_csv(
"tests/f1.bed",
sep="\t",
header=None,
names="Chromosome Start End Name Score Strand".split())
return PyRanges(df)
@pytest.fixture
def f2(names):
df = pd.read_csv("tests/f2.bed", sep="\t", header=None, names=names)
return PyRanges(df)
@pytest.fixture
def chromsizes():
from io import StringIO
df = pd.read_csv(
StringIO("""
chr1 249250621
chr2 243199373
chr3 198022430
chr4 191154276
chr5 180915260
chr6 171115067
chr7 159138663
chrX 155270560
chr8 146364022
chr9 141213431
chr10 135534747
chr11 135006516
chr12 133851895
chr13 115169878
chr14 107349540
chr15 102531392
chr16 90354753
chr17 81195210
chr18 78077248
chr20 63025520
chrY 59373566
chr19 59128983
chr22 51304566
chr21 48129895"""),
sep="\s+",
header=None,
index_col=0)
df.insert(0, "Start", 0)
df = df.reset_index()
df.columns = ["Chromosome", "Start", "End"]
return PyRanges(df)
|
