def test_write(self): """ Check if VCFtools allele frequencies are correctly written to the output file. """ with open(self.__input_file) as input_file, open(self.__output_file, "w") as output_file: writer = Writer(output_file) for record in Reader(input_file).variants(): writer.write(record) # compare the test output file to the original one with open(self.__input_file) as input_file, open(self.__output_file) as output_file: for x, y in zip(Reader(input_file).variants(), Reader(output_file).variants()): self.assertEqual(x, y) os.unlink(self.__output_file)
def test_variants(self): """ Check if SortedReader reads and sorts variants. """ with open(self.__unsorted) as unsorted_input, open(self.__output, "w") as sorted_output: reader = SortedReader(unsorted_input) writer = Writer(sorted_output) for chromosome in reader.variants: for variant in reader.variants[chromosome]: writer.write(variant) # compare the original sorted file and the produced one with open(self.__sorted) as original_sorted, open(self.__output) as produced_sorted: for x, y in zip(Reader(original_sorted).variants(), Reader(produced_sorted).variants()): self.assertEqual(x, y) os.unlink(self.__output)
def test_write(self): """ Check if VCFtools allele frequencies are correctly written to the output file. """ with open(self.__input_file) as input_file, \ open(self.__output_file, 'w') as output_file: writer = Writer(output_file) for record in Reader(input_file).variants(): writer.write(record) # compare the test output file to the original one with open(self.__input_file) as input_file, \ open(self.__output_file) as output_file: for x, y in zip( Reader(input_file).variants(), Reader(output_file).variants()): self.assertEqual(x, y)
def test_variants(self): """ Check if SortedReader reads and sorts variants. """ with open(self.__unsorted) as unsorted_input, \ open(self.__output, 'w') as sorted_output: reader = SortedReader(unsorted_input) writer = Writer(sorted_output) for chromosome in reader.variants: for variant in reader.variants[chromosome]: writer.write(variant) # compare the original sorted file and the produced one with open(self.__sorted) as original_sorted, \ open(self.__output) as produced_sorted: for x, y in zip( Reader(original_sorted).variants(), Reader(produced_sorted).variants()): self.assertEqual(x, y)