def test_sniff_correct(self):
valid_xml = os.path.join(os.path.dirname(__file__), "mikado.blast.xml")
valid, header, exc = blast_utils.BlastOpener(valid_xml).sniff()
self.assertTrue(valid, (valid, exc))
self.assertIsNone(exc, exc)
with open(valid_xml, mode="rt") as new_handle:
valid, header, exc = blast_utils.BlastOpener(new_handle).sniff()
self.assertTrue(valid, (valid, exc))
self.assertIsNone(exc, exc)
def test_sniff_gzip(self):
new = gzip.open(tempfile.mktemp(suffix=".xml.gz"), mode="wt")
valid_xml = os.path.join(os.path.dirname(__file__), "mikado.blast.xml")
with open(valid_xml) as vx:
for line in vx:
new.write(line)
new.flush()
valid, header, exc = blast_utils.BlastOpener(new.name).sniff()
self.assertTrue(valid, (valid, exc))
self.assertIsNone(exc, exc)
with gzip.open(new.name, mode="rt") as new_handle:
valid, header, exc = blast_utils.BlastOpener(new_handle).sniff()
self.assertTrue(valid, (valid, exc))
self.assertIsNone(exc, exc)
def test_fail_closed(self):
valid_xml = os.path.join(os.path.dirname(__file__), "mikado.blast.xml")
opener = blast_utils.BlastOpener(valid_xml)
opener.close()
with self.assertRaises(ValueError):
opener.sniff()
def test_sniff_invalid(self):
invalid_xml = tempfile.NamedTemporaryFile(delete=False)
invalid_xml.write(b"failing\n")
# print(b"failing", file=invalid_xml)
invalid_xml.close()
with self.assertRaises(ValueError):
valid, header, exc = blast_utils.BlastOpener(
invalid_xml.name).sniff()
os.remove(invalid_xml.name)
def test_asn(self):
master = os.getcwd()
os.chdir(os.path.dirname(__file__))
valid_asn = "mikado.blast.asn"
with gzip.open("{0}.gz".format(valid_asn), "rt") as comp_asn:
with open(valid_asn, "wt") as asn:
for line in comp_asn:
asn.write(line)
with open("uniprot_sprot_plants.fasta", "wt") as uni_out:
with gzip.open("uniprot_sprot_plants.fasta.gz", "rt") as uni:
for line in uni:
uni_out.write(line)
subprocess.call(
"makeblastdb -in uniprot_sprot_plants.fasta -dbtype=prot".format(
os.path.dirname(__file__)),
shell=True,
stderr=subprocess.DEVNULL,
stdout=subprocess.DEVNULL)
valid, header, exc = blast_utils.BlastOpener(valid_asn).sniff()
self.assertTrue(valid, (valid, exc))
self.assertIsNone(exc, exc)
valid, header, exc = blast_utils.BlastOpener(
"{0}.gz".format(valid_asn)).sniff()
self.assertTrue(valid, (valid, exc))
self.assertIsNone(exc, exc)
# This should fix the issue of blast_formatter crashing
time.sleep(1)
for fname in os.listdir("."):
if "uniprot_sprot_plants.fasta" in fname and not fname.endswith(
".gz"):
os.remove(fname)
os.remove(valid_asn)
os.chdir(master)
def test_sniff_inexistent(self):
inexistent_xml = tempfile.mktemp()
with self.assertRaises(OSError):
valid, header, exc = blast_utils.BlastOpener(
inexistent_xml).sniff()