def test_prepare_trinity_gff(self):
self.conf["prepare"]["files"]["labels"].append("tr")
self.conf["prepare"]["files"]["output_dir"] = tempfile.gettempdir()
args = Namespace()
args.json_conf = self.conf
for test_file in ("trinity.gff3",
"trinity.match_matchpart.gff3",
"trinity.cDNA_match.gff3",
"trinity.gtf"):
with self.subTest(test_file=test_file):
self.conf["prepare"]["files"]["gff"] = [pkg_resources.resource_filename("Mikado.tests",
test_file)]
prepare.prepare(args, self.logger)
# Now that the program has run, let's check the output
fa = pyfaidx.Fasta(os.path.join(self.conf["prepare"]["files"]["output_dir"],
"mikado_prepared.fasta"))
res = dict((_, len(fa[_])) for _ in fa.keys())
fa.close()
self.assertEqual(res, self.trinity_res)
os.remove(os.path.join(self.conf["prepare"]["files"]["output_dir"],
"mikado_prepared.fasta.fai"))
def test_prepare_trinity_gff(self):
self.conf["prepare"]["files"]["labels"].append("tr")
self.conf["prepare"]["files"]["output_dir"] = tempfile.gettempdir()
args = Namespace()
args.json_conf = self.conf
for test_file in ("trinity.gff3", "trinity.match_matchpart.gff3",
"trinity.cDNA_match.gff3", "trinity.gtf"):
with self.subTest(test_file=test_file):
self.conf["prepare"]["files"]["gff"] = [
pkg_resources.resource_filename("Mikado.tests", test_file)
]
prepare.prepare(args, self.logger)
# Now that the program has run, let's check the output
fa = pyfaidx.Fasta(
os.path.join(self.conf["prepare"]["files"]["output_dir"],
"mikado_prepared.fasta"))
res = dict((_, len(fa[_])) for _ in fa.keys())
fa.close()
self.assertEqual(res, self.trinity_res)
os.remove(
os.path.join(self.conf["prepare"]["files"]["output_dir"],
"mikado_prepared.fasta.fai"))
def test_prepare_trinity_and_cufflinks(self):
self.conf["prepare"]["files"]["labels"] = ["cl", "tr"]
self.conf["prepare"]["files"]["gff"].append(
pkg_resources.resource_filename("Mikado.tests", "cufflinks.gtf"))
self.conf["prepare"]["files"]["gff"].append("")
self.conf["prepare"]["files"]["output_dir"] = tempfile.gettempdir()
self.conf["prepare"]["files"]["out_fasta"] = "mikado_prepared.fasta"
self.conf["prepare"]["files"]["out"] = "mikado_prepared.gtf"
args = Namespace()
args.json_conf = self.conf
for test_file in ("trinity.gff3", "trinity.match_matchpart.gff3",
"trinity.cDNA_match.gff3", "trinity.gtf"):
with self.subTest(test_file=test_file):
self.conf["prepare"]["files"]["gff"][
1] = pkg_resources.resource_filename(
"Mikado.tests", test_file)
self.conf["prepare"]["files"][
"out_fasta"] = "mikado_prepared.fasta"
self.conf["prepare"]["files"]["out"] = "mikado_prepared.gtf"
prepare.prepare(args, self.logger)
# Now that the program has run, let's check the output
self.assertTrue(
os.path.exists(
os.path.join(
self.conf["prepare"]["files"]["output_dir"],
"mikado_prepared.fasta")))
self.assertGreater(
os.stat(
os.path.join(
self.conf["prepare"]["files"]["output_dir"],
"mikado_prepared.fasta")).st_size, 0)
fa = pyfaidx.Fasta(
os.path.join(self.conf["prepare"]["files"]["output_dir"],
"mikado_prepared.fasta"))
res = dict((_, len(fa[_])) for _ in fa.keys())
fa.close()
precal = self.trinity_res.copy()
precal.update(self.cuff_results)
self.assertEqual(res, precal)
os.remove(
os.path.join(self.conf["prepare"]["files"]["output_dir"],
"mikado_prepared.fasta.fai"))
def test_prepare_trinity_and_cufflinks(self):
self.conf["prepare"]["files"]["labels"] = ["cl", "tr"]
self.conf["prepare"]["files"]["gff"].append(pkg_resources.resource_filename("Mikado.tests",
"cufflinks.gtf"))
self.conf["prepare"]["files"]["gff"].append("")
self.conf["prepare"]["files"]["output_dir"] = tempfile.gettempdir()
self.conf["prepare"]["files"]["out_fasta"] = "mikado_prepared.fasta"
self.conf["prepare"]["files"]["out"] = "mikado_prepared.gtf"
args = Namespace()
args.json_conf = self.conf
for test_file in ("trinity.gff3",
"trinity.match_matchpart.gff3",
"trinity.cDNA_match.gff3",
"trinity.gtf"):
with self.subTest(test_file=test_file):
self.conf["prepare"]["files"]["gff"][1] = pkg_resources.resource_filename("Mikado.tests",
test_file)
self.conf["prepare"]["files"]["out_fasta"] = "mikado_prepared.fasta"
self.conf["prepare"]["files"]["out"] = "mikado_prepared.gtf"
prepare.prepare(args, self.logger)
# Now that the program has run, let's check the output
self.assertTrue(os.path.exists(os.path.join(self.conf["prepare"]["files"]["output_dir"],
"mikado_prepared.fasta")))
self.assertGreater(os.stat(os.path.join(self.conf["prepare"]["files"]["output_dir"],
"mikado_prepared.fasta")).st_size, 0)
fa = pyfaidx.Fasta(os.path.join(self.conf["prepare"]["files"]["output_dir"],
"mikado_prepared.fasta"))
res = dict((_, len(fa[_])) for _ in fa.keys())
fa.close()
precal = self.trinity_res.copy()
precal.update(self.cuff_results)
self.assertEqual(res, precal)
os.remove(os.path.join(self.conf["prepare"]["files"]["output_dir"],
"mikado_prepared.fasta.fai"))