def test_write_lines(self):
with TempDirectory() as output_file:
writer = FileWriter(os.path.join(output_file.path, "A.tmp"))
writer.open()
writer.write("1\n2\n")
writer.write("3")
writer.close()
actual_file = open(os.path.join(output_file.path, "A.tmp"))
actual_output = actual_file.readlines()
actual_file.close()
self.assertEquals(["1\n", "2\n", "3"], actual_output)
def test_write_lines(self):
with TempDirectory() as output_file:
writer = FileWriter(os.path.join(output_file.path, "A.tmp"))
writer.open()
writer.write("1\n2\n")
writer.write("3")
writer.close()
actual_file = open(os.path.join(output_file.path, "A.tmp"))
actual_output = actual_file.readlines()
actual_file.close()
self.assertEquals(["1\n", "2\n", "3"], actual_output)
def test_write(self):
with TempDirectory() as output_file:
file_path = os.path.join(output_file.path, "test.tmp")
writer = FileWriter(file_path)
writer.open()
writer.write("A")
writer.write("B\n")
writer.write("CD\n")
writer.close()
actual_output = output_file.read('test.tmp', encoding='utf8')
expected_output = "AB|CD|".replace('|', os.linesep)
self.assertEquals(expected_output, actual_output)
def test_write(self):
with TempDirectory() as output_file:
file_path = os.path.join(output_file.path, "test.tmp")
writer = FileWriter(file_path)
writer.open()
writer.write("A")
writer.write("B\n")
writer.write("CD\n")
writer.close()
actual_output = output_file.read("test.tmp", encoding="utf8")
expected_output = "AB|CD|".replace("|", os.linesep)
self.assertEquals(expected_output, actual_output)
def _sort_vcf(reader, sorted_dir):
vcf_records = []
reader.open()
for vcf_record in reader.vcf_records():
vcf_records.append(vcf_record)
reader.close()
vcf_records.sort()
writer = FileWriter(os.path.join(sorted_dir, reader.file_name))
writer.open()
writer.write("\n".join(reader.metaheaders) + "\n")
writer.write(reader.column_header + "\n")
for vcf_record in vcf_records:
writer.write(vcf_record.text())
writer.close()
reader = MergeVcfReader(vcf.FileReader(writer.output_filepath))
return reader
def _sort_vcf(reader, sorted_dir):
vcf_records = []
reader.open()
for vcf_record in reader.vcf_records():
vcf_records.append(vcf_record)
reader.close()
vcf_records.sort()
writer = FileWriter(os.path.join(sorted_dir,
reader.file_name))
writer.open()
writer.write("\n".join(reader.metaheaders) + "\n")
writer.write(reader.column_header + "\n")
for vcf_record in vcf_records:
writer.write(vcf_record.text())
writer.close()
reader = MergeVcfReader(vcf.FileReader(writer.output_filepath))
return reader
