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)