def get_missing_chromosomes(self):
missing_chromosomes = []
for name, length in Chromosome.sorted_chromosome_length_tuples(self.assembly):
chromosome = Chromosome(name, self.assembly)
filepath = chromosome.path()
if not chromosome.exists():
missing_chromosomes.append(name)
else:
expected_size = length + len(chromosome.header()) + 1
size = os.path.getsize(filepath)
if size != expected_size:
self.log('Removing mismatched chromosome %s' % name)
missing_chromosomes.append(name)
os.remove(filepath)
return missing_chromosomes
def get_missing_chromosomes(self):
missing_chromosomes = []
for name, length in Chromosome.sorted_chromosome_length_tuples(
self.assembly):
chromosome = Chromosome(name, self.assembly)
filepath = chromosome.path()
if not chromosome.exists():
missing_chromosomes.append(name)
else:
expected_size = length + len(chromosome.header()) + 1
size = os.path.getsize(filepath)
if size != expected_size:
self.log('Removing mismatched chromosome %s' % name)
missing_chromosomes.append(name)
os.remove(filepath)
return missing_chromosomes
