def test_lasv_oob_clip(self):
input_dir = os.path.join(self.input_dir, "lasv", "input")
expected_dir = os.path.join(self.input_dir, "lasv", "expected")
temp_dir = tempfile.gettempdir()
infastas = [
os.path.join(input_dir, f) for f in [
"align_mafft-ref-lasv-ISTH2376_1.fasta",
"align_mafft-ref-lasv-ISTH2376_2.fasta"
]
]
intables = [
os.path.join(input_dir, f)
for f in ["KM821997.1.tbl", "KM821998.1.tbl"]
]
out_table_names = [
"LASV_NGA_2018_0026-1.tbl", "LASV_NGA_2018_0026-2.tbl",
"LASV_NGA_2018_0097-1.tbl", "LASV_NGA_2018_0097-2.tbl",
"LASV_NGA_2018_0541-1.tbl", "LASV_NGA_2018_0541-2.tbl",
"LASV_NGA_2018_0611-1.tbl", "LASV_NGA_2018_0611-2.tbl",
"LASV_NGA_2018_0664-1.tbl", "LASV_NGA_2018_0664-2.tbl",
"LASV_NGA_2018_0959-1.tbl", "LASV_NGA_2018_0959-2.tbl",
"LASV_NGA_2018_0998-1.tbl", "LASV_NGA_2018_0998-2.tbl",
"LASV_NGA_2018_1024-1.tbl", "LASV_NGA_2018_1024-2.tbl",
"LASV_NGA_2018_1079-1.tbl", "LASV_NGA_2018_1079-2.tbl",
"LASV_NGA_2018_1177-1.tbl", "LASV_NGA_2018_1177-2.tbl",
"LASV_NGA_2018_1375-1.tbl", "LASV_NGA_2018_1375-2.tbl",
"LASV_NGA_2018_1381-1.tbl", "LASV_NGA_2018_1381-2.tbl",
"LASV_NGA_2018_1392-1.tbl", "LASV_NGA_2018_1392-2.tbl",
"LASV_NGA_2018_1643-1.tbl", "LASV_NGA_2018_1643-2.tbl"
]
out_tbls = [os.path.join(temp_dir, f) for f in out_table_names]
expected_tbls = [
os.path.join(expected_dir, f) for f in out_table_names
]
for i in range(0, len(infastas)):
ncbi.tbl_transfer_prealigned(infastas[i],
os.path.join(
input_dir,
"ref-lasv-ISTH2376.fasta"),
intables,
temp_dir,
oob_clip=True)
for i in range(0, len(out_table_names)):
out_tbl = out_tbls[i]
expected_tbl = expected_tbls[i]
assert_equal_contents(self, out_tbl, expected_tbl)
def test_synthetic_feature_table(self):
input_dir = os.path.join(self.input_dir, "synthetic", "input")
expected_dir = os.path.join(self.input_dir, "synthetic", "expected")
temp_dir = tempfile.gettempdir()
in_tbl = os.path.join(input_dir, "ref.tbl")
out_tbl = os.path.join(temp_dir, "sample.tbl")
expected = os.path.join(expected_dir, "mapped.tbl")
ncbi.tbl_transfer_prealigned(
os.path.join(input_dir, "aligned_1.fasta"),
os.path.join(input_dir, "ref.fasta"), [in_tbl], temp_dir)
assert_equal_contents(self, out_tbl, expected)
def test_synthetic_feature_table(self):
input_dir = os.path.join(self.input_dir, "synthetic", "input")
expected_dir = os.path.join(self.input_dir, "synthetic", "expected")
temp_dir = tempfile.gettempdir()
in_tbl = os.path.join(input_dir,"ref.tbl")
out_tbl = os.path.join(temp_dir,"sample.tbl")
expected = os.path.join(expected_dir, "mapped.tbl")
ncbi.tbl_transfer_prealigned(
os.path.join(input_dir,"aligned_1.fasta"),
os.path.join(input_dir,"ref.fasta"),
[in_tbl],
temp_dir)
assert_equal_contents(self, out_tbl, expected)
def test_lasv_oob_clip(self):
input_dir = os.path.join(self.input_dir, "lasv", "input")
expected_dir = os.path.join(self.input_dir, "lasv", "expected")
temp_dir = tempfile.gettempdir()
infastas = [os.path.join(input_dir, f) for f in [
"align_mafft-ref-lasv-ISTH2376_1.fasta",
"align_mafft-ref-lasv-ISTH2376_2.fasta"
]
]
intables =[os.path.join(input_dir, f) for f in [
"KM821997.1.tbl",
"KM821998.1.tbl"
]
]
out_table_names = [
"LASV_NGA_2018_0026-1.tbl",
"LASV_NGA_2018_0026-2.tbl",
"LASV_NGA_2018_0097-1.tbl",
"LASV_NGA_2018_0097-2.tbl",
"LASV_NGA_2018_0541-1.tbl",
"LASV_NGA_2018_0541-2.tbl",
"LASV_NGA_2018_0611-1.tbl",
"LASV_NGA_2018_0611-2.tbl",
"LASV_NGA_2018_0664-1.tbl",
"LASV_NGA_2018_0664-2.tbl",
"LASV_NGA_2018_0959-1.tbl",
"LASV_NGA_2018_0959-2.tbl",
"LASV_NGA_2018_0998-1.tbl",
"LASV_NGA_2018_0998-2.tbl",
"LASV_NGA_2018_1024-1.tbl",
"LASV_NGA_2018_1024-2.tbl",
"LASV_NGA_2018_1079-1.tbl",
"LASV_NGA_2018_1079-2.tbl",
"LASV_NGA_2018_1177-1.tbl",
"LASV_NGA_2018_1177-2.tbl",
"LASV_NGA_2018_1375-1.tbl",
"LASV_NGA_2018_1375-2.tbl",
"LASV_NGA_2018_1381-1.tbl",
"LASV_NGA_2018_1381-2.tbl",
"LASV_NGA_2018_1392-1.tbl",
"LASV_NGA_2018_1392-2.tbl",
"LASV_NGA_2018_1643-1.tbl",
"LASV_NGA_2018_1643-2.tbl"
]
out_tbls =[os.path.join(temp_dir, f) for f in out_table_names]
expected_tbls = [os.path.join(expected_dir, f) for f in out_table_names]
for i in range(0, len(infastas)):
ncbi.tbl_transfer_prealigned(
infastas[i],
os.path.join(input_dir,"ref-lasv-ISTH2376.fasta"),
intables,
temp_dir,
oob_clip=True)
for i in range(0,len(out_table_names)):
out_tbl = out_tbls[i]
expected_tbl = expected_tbls[i]
assert_equal_contents(self, out_tbl, expected_tbl)
