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)
