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