diff --git a/reads_consensus_class.py b/reads_consensus_class.py index a028e8c2ca5e4b3fef4d04acc7e3f23401c24d4d..2a597cc36df85fd3758d4923c0c81b5f68e0b712 100755 --- a/reads_consensus_class.py +++ b/reads_consensus_class.py @@ -65,8 +65,8 @@ def consensus_class_init(kmer_occ_dict: dict, kmer_size: int, start_primer: str, start_kmer_score_occ = Consensus.kmer_occurrences_dict[start_kmer] Consensus.list_of_consensus_to_explore.append([start_kmer_score_occ, "start", 0, start_kmer]) - # continue to explore new consensus, but stop at 10 000 consensus (arbitrary) - while Consensus.list_of_consensus_to_explore != [] and Consensus.consensus_number <= 10000: + # continue to explore new consensus + while Consensus.list_of_consensus_to_explore:# and Consensus.consensus_number <= 30000: [score, father_name, split_index, start_kmer] = Consensus.list_of_consensus_to_explore.pop() # get last element # the one with higher score create_new_consensus(father_name, split_index, start_kmer) # run the new consensus @@ -597,7 +597,7 @@ def kmer_consensus(input_path: str, output_path: str, start_primer: str, stop_pr #print("paths creation " +str(round(consensus_time, 3))) start = time.time() # remove the consensus of len <= kmer size, because they are created only out of 1 error on a kmer - dump_short_consensus() + #dump_short_consensus() dumping_time = time.time() - start #print("dump paths "+str(round(dumping_time, 3)))