def test1_3(self):
input_vcf = self.strelka_vcf
class_name = type(self).__name__
test_name = sys._getframe().f_code.co_name
output_vcf = os.path.join(self.OUTPUT_FOLDER, "%s.%s.vcf" % (class_name, test_name))
vcf_transformer = StrelkaVcfDedupper(input_vcf, output_vcf, VariantComparerNoAlternate(),
SELECTION_METHOD_QUALITY, 1)
vcf_transformer.process_vcf()
del vcf_transformer
def test1_0_1(self):
input_vcf = self.strelka_vcf
class_name = type(self).__name__
test_name = sys._getframe().f_code.co_name
output_vcf = os.path.join(self.OUTPUT_FOLDER, "%s.%s.vcf" % (class_name, test_name))
vcf_transformer = StrelkaVcfDedupper(input_vcf, output_vcf, VariantComparerNoAlternate(),
SELECTION_METHOD_AF, 1, "none")
try:
vcf_transformer.process_vcf()
self.assertTrue(False)
except VcfFormatError:
self.assertTrue(True)
del vcf_transformer
def run(self):
logging.info("Starting the VCF duplication removal...")
if self.sort_vcf:
# sorts the input VCF
self.__sort()
else:
# assumes input is sorted
self.sorted_vcf = self.input_vcf
# selects the appropriate comparer
if self.equality_mode == INCLUDE_ALTERNATE:
comparer = VariantComparerWithAlternate()
elif self.equality_mode == EXCLUDE_ALTERNATE:
comparer = VariantComparerNoAlternate()
# selects the appropriate transformer
if self.variant_caller == STRELKA_VARIANT_CALLER:
transformer = StrelkaVcfDedupper(self.sorted_vcf, self.output_vcf,
comparer, self.selection_method,
self.sample_idx, self.sample_name)
elif self.variant_caller == STARLING_VARIANT_CALLER:
transformer = StarlingVcfDedupper(self.sorted_vcf, self.output_vcf,
comparer, self.selection_method,
self.sample_idx,
self.sample_name)
elif self.variant_caller == PLATYPUS_VARIANT_CALLER:
transformer = PlatypusVcfDedupper(self.sorted_vcf, self.output_vcf,
comparer, self.selection_method)
elif self.variant_caller == GENERIC_VARIANT_CALLER:
transformer = GenericVcfDedupper(self.sorted_vcf, self.output_vcf,
comparer, self.selection_method)
elif self.variant_caller == DUPLICATION_FINDER:
transformer = DuplicationFinder(self.sorted_vcf, self.output_vcf,
comparer)
# run the transformation
transformer.process_vcf()
# forces closing the resources
transformer.__del__()
# delete temporary files
if self.sort_vcf:
os.remove(self.sorted_vcf)
logging.info("Duplication removal finished!")