import pytest
import os
def pytest_configure(config):
os.chdir(os.path.dirname(__file__))
os.makedirs("results", exist_ok=True)
@pytest.fixture
def reference_path():
# download chr4 from ucsc if needed
reference_path = "data/chr4.fa"
if not os.path.exists(reference_path):
import urllib.request
import zlib
url = "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr4.fa.gz"
resource = urllib.request.urlopen(url)
with open(reference_path, "w") as outf:
data = zlib.decompress(resource.read(), 16+zlib.MAX_WBITS).decode("utf-8")
outf.write(data)
return reference_path
@pytest.fixture
def bam_doc():
import genomeview
source = genomeview.FastaGenomeSource(reference_path())
doc = genomeview.Document(900)
view = genomeview.GenomeView("chr4", 96549060, 96549060+250, "+", source)
doc.add_view(view)
bam_track_hg002 = genomeview.SingleEndBAMTrack("data/quick_consensus_test.bam", name="HG002")
bam_track_hg002.min_indel_size = 3
view.add_track(bam_track_hg002)
axis_track = genomeview.Axis()
view.add_track(axis_track)
return doc
