def test_format_map_file(self): """format_map_file should produce correct result""" desc_key = "Description" sample_id = "SampleID" headers = ['SampleID', 'a', 'Description', 'b'] id_map = {'x': {'a': 3, 'b': 4}, 'y': {'a': 5, 'b': 6}} desc_map = {'x': 'sample x', 'y': 'sample y'} run_desc = 'run desc' self.assertEqual( format_map_file(headers, id_map, desc_key, sample_id, desc_map, run_desc), """#SampleID\ta\tb\tDescription #run desc x\t3\t4\tsample x y\t5\t6\tsample y""")
def test_format_map_file(self): """format_map_file should produce correct result""" desc_key = "Description" sample_id = "SampleID" headers = ['SampleID', 'a', 'Description', 'b'] id_map = {'x':{'a':3,'b':4}, 'y':{'a':5,'b':6}} desc_map = {'x':'sample x','y':'sample y'} run_desc = 'run desc' self.assertEqual(format_map_file(headers, id_map, desc_key, sample_id,\ desc_map, run_desc), """#SampleID\ta\tb\tDescription #run desc x\t3\t4\tsample x y\t5\t6\tsample y""")
def test_format_map_file(self): """format_map_file should produce correct result""" desc_key = "Description" sample_id = "SampleID" headers = ["SampleID", "a", "Description", "b"] id_map = {"x": {"a": 3, "b": 4}, "y": {"a": 5, "b": 6}} desc_map = {"x": "sample x", "y": "sample y"} run_desc = "run desc" self.assertEqual( format_map_file(headers, id_map, desc_key, sample_id, desc_map, run_desc), """#SampleID\ta\tb\tDescription #run desc x\t3\t4\tsample x y\t5\t6\tsample y""", )
def write_corrected_file(headers, id_map, description_map, run_description, \ output_filepath, chars_replaced=False): """ Writes corrected mapping file with illegal characters replaced """ outf = open(output_filepath, 'w') if chars_replaced: outfile_data=format_map_file(headers, id_map, DESC_KEY, SAMPLE_ID_KEY,\ description_map, run_description) else: outfile_data="# No invalid characters were found and replaced.\n"+\ "# Note that non-IUPAC DNA characters found in primer or barcode\n"+\ "# sequences are not replaced but will be listed in the .log file." for data in outfile_data: outf.write(data) return
def write_corrected_file(headers, id_map, description_map, run_description, output_filepath, chars_replaced=False): """ Writes corrected mapping file with illegal characters replaced """ outf = open(output_filepath, "w") if chars_replaced: outfile_data = format_map_file(headers, id_map, DESC_KEY, SAMPLE_ID_KEY, description_map, run_description) else: outfile_data = ( "# No invalid characters were found and replaced.\n" + "# Note that non-IUPAC DNA characters found in primer or barcode\n" + "# sequences are not replaced but will be listed in the .log file." ) for data in outfile_data: outf.write(data) return