Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
def count_homopolymers(args):
os.mkdir(args.output_dir)
score = AverageScore()
headers = [
'query_name', 'ref_name', 'ref_start', 'rev_comp', 'query_start',
'ref_base', 'query_base', 'ref_len', 'query_len']
prefix = os.path.join(args.output_dir, 'hp')
with open(prefix + '_catalogue.txt', 'w') as txt_fh:
txt_fh.write('\t'.join(headers) + "\n")
score, counts = process_bam(args.bam, txt_fh, args.homo_len, score)
print("Found {} homopolymers in {}. Average score: {}".format(
score.count, args.bam, score))
save_counts(counts, prefix + '_counts.pkl')
analyse_counts(counts, prefix)
def __add__(self, score):
if isinstance(score, AverageScore):
self.cumulative_score += score.cumulative_score
self.count += score.count
else:
self.cumulative_score += score
self.count += 1
return self