def genome(request, tempdir):
"""Create a test genome."""
name = "dm3" # Use fake name for blacklist test
fafile = "tests/data/small_genome.fa"
# Input needs to be bgzipped, depending on param
if os.path.exists(fafile + ".gz"):
if request.param == "unzipped":
check_call(["gunzip", fafile + ".gz"])
elif request.param == "bgzipped":
check_call(["bgzip", fafile])
tmpdir = os.path.join(tempdir, request.param, name)
os.makedirs(tmpdir)
if request.param == "bgzipped":
fafile += ".gz"
copyfile(fafile, os.path.join(tmpdir, os.path.basename(fafile)))
for p in init_plugins():
activate(p)
# provide the fixture value
yield Genome(name, genome_dir=os.path.join(tempdir, request.param))
if os.path.exists(fafile) and request.param == "unzipped":
check_call(["bgzip", fafile])
def test_plugins():
# activate and check all plugins
for p in init_plugins():
if p not in ["blacklist", "star"]:
assert genomepy.utils.cmd_ok(p)
elif p == "star":
assert genomepy.utils.cmd_ok(p.upper())
activate(p)
def genome(tempdir):
"""Create a test genome."""
name = "small_genome"
fafile = "tests/data/small_genome.fa"
if os.path.exists(fafile + ".gz"):
check_call(["gunzip", fafile + ".gz"])
os.mkdir(os.path.join(tempdir, name))
copyfile(fafile, os.path.join(tempdir, name, os.path.basename(fafile)))
for p in init_plugins():
activate(p)
yield Genome(name, genome_dir=tempdir) # provide the fixture value
if os.path.exists(fafile):
check_call(["gzip", fafile])