def test_retrieve_uniprot(self):
go.Gff3Parser = Mock_gff_parser
database_file = os.path.join(self.test_folder, "database")
gen_file(database_file, self.example.idmapping)
gff_file = os.path.join(self.test_folder, "test.gff")
gen_file(gff_file, "test")
out_file = os.path.join(self.test_folder, "out.gff")
tran_file = os.path.join(self.test_folder, "test_transcript.gff")
gen_file(tran_file, "test")
go.retrieve_uniprot(database_file, gff_file, out_file, tran_file, "express")
datas = import_data(out_file)
self.assertEqual(set(datas), set(self.example.out_retrieve.split("\n")))
def test_retrieve_uniprot(self):
go.Gff3Parser = Mock_gff_parser
database_file = os.path.join(self.test_folder, "database")
gen_file(database_file, self.example.idmapping)
gff_file = os.path.join(self.test_folder, "test.gff")
gen_file(gff_file, "test")
out_file = os.path.join(self.test_folder, "out.gff")
tran_file = os.path.join(self.test_folder, "test_transcript.gff")
gen_file(tran_file, "test")
go.retrieve_uniprot(database_file, gff_file, out_file, tran_file,
"express")
datas = import_data(out_file)
self.assertEqual(set(datas),
set(self.example.out_retrieve.split("\n")))
def _retrieve_go(self, uniprot, out_path, type_):
prefixs = []
for gff in os.listdir(self.gff_path):
prefix = gff.replace(".gff", "")
prefixs.append(prefix)
self.helper.check_make_folder(os.path.join(out_path, prefix))
out_file = os.path.join(out_path, prefix,
"_".join([prefix, "uniprot.csv"]))
print("Extracting GO terms of {0} from UniProt".format(prefix))
if self.tran_path is not None:
tran_file = os.path.join(self.tran_path,
"_".join([prefix, "transcript.gff"]))
else:
tran_file = None
retrieve_uniprot(uniprot, os.path.join(self.gff_path, gff),
out_file, tran_file, type_)
def _retrieve_go(self, uniprot, out_path, type_):
prefixs = []
for gff in os.listdir(self.gff_path):
prefix = gff.replace(".gff", "")
prefixs.append(prefix)
self.helper.check_make_folder(os.path.join(out_path, prefix))
out_file = os.path.join(out_path, prefix,
"_".join([prefix, "uniprot.csv"]))
print("extracting Go terms of {0} from UniProt...".format(prefix))
if self.tran_path is not None:
tran_file = os.path.join(self.tran_path,
"_".join([prefix, "transcript.gff"]))
else:
tran_file = None
retrieve_uniprot(uniprot, os.path.join(self.gff_path, gff),
out_file, tran_file, type_)
def _retrieve_go(self, uniprot, out_path, type_, log):
prefixs = []
log.write("Running gene_ontology.py to retrieve GO terms.\n")
for gff in os.listdir(self.gff_path):
prefix = gff.replace(".gff", "")
prefixs.append(prefix)
self.helper.check_make_folder(os.path.join(out_path, prefix))
out_file = os.path.join(out_path, prefix,
"_".join([prefix, "uniprot.csv"]))
print("Extracting GO terms of {0} from UniProt".format(prefix))
if self.tran_path is not None:
tran_file = os.path.join(self.tran_path,
"_".join([prefix, "transcript.gff"]))
else:
tran_file = None
retrieve_uniprot(uniprot, os.path.join(self.gff_path, gff),
out_file, tran_file, type_)
log.write("\t" + out_file + " is generated.\n")
def _retrieve_go(self, uniprot, out_path, type_, log):
prefixs = []
log.write("Running gene_ontology.py to retrieve GO terms.\n")
for gff in os.listdir(self.gff_path):
prefix = gff.replace(".gff", "")
prefixs.append(prefix)
self.helper.check_make_folder(os.path.join(out_path, prefix))
out_file = os.path.join(out_path, prefix,
"_".join([prefix, "uniprot.csv"]))
print("Extracting GO terms of {0} from UniProt".format(prefix))
if self.tran_path is not None:
tran_file = os.path.join(self.tran_path,
"_".join([prefix, "transcript.gff"]))
else:
tran_file = None
retrieve_uniprot(uniprot, os.path.join(self.gff_path, gff),
out_file, tran_file, type_)
log.write("\t" + out_file + " is generated.\n")