def test_constructor_invalid_gff_path(self):
invalid_path_ext = os.path.join(os.getcwd(), 'test', 'data',
'test_data', 'Breviolum_minutum.txt')
non_existant_path = os.path.join(os.getcwd(), 'test', 'data',
'test_data', 'Breviolum_minutum.gff')
try:
sequencing.FlatFileCreator("SYMB1", "teamcx", invalid_path_ext)
except OSError:
# Correct error
pass
except Exception:
self.fail()
else:
self.fail()
try:
sequencing.FlatFileCreator("SYMB1", "teamcx", non_existant_path)
except OSError:
# Correct error
pass
except Exception:
self.fail()
else:
self.fail()
def test_single_get_gene_dict(self):
cls = self.__class__
test_ffc = sequencing.FlatFileCreator("SYMB1", "teamcx",
cls.gff_path_1)
# Expected output
expected = {"Bmin.gene1": (0, 55)}
self.assertEqual(test_ffc.get_gene_dict(), expected)
def test_1_gene_str(self):
cls = self.__class__
gene_seq_1 = sequencing.GeneSequence("SYMB1", "teamcx", cls.gff_1, 1,
"Bmin.gene1", 0, 55)
expected = str(gene_seq_1)
ffc_test = sequencing.FlatFileCreator("SYMB1", "teamcx",
cls.gff_path_1)
self.assertEqual(str(ffc_test), expected)
def test_simple_str(self):
cls = self.__class__
gene_seq_1 = sequencing.GeneSequence("SYMB1", "teamcx", cls.short_gff,
1, "Bmin.gene1", 0, 55)
gene_seq_2 = sequencing.GeneSequence("SYMB1", "teamcx", cls.short_gff,
2, "Bmin.gene2", 56, 165)
expected = str(gene_seq_1) + '\n' + str(gene_seq_2)
ffc_test = sequencing.FlatFileCreator("SYMB1", "teamcx",
cls.short_gff_path)
self.assertEqual(str(ffc_test), expected)
def test_constructor(self):
cls = self.__class__
sequencing.FlatFileCreator("SYMB1", "teamcx", cls.short_gff_path)