diff --git a/piranha/analysis/phylo_functions.py b/piranha/analysis/phylo_functions.py index c6268b2..f70524e 100644 --- a/piranha/analysis/phylo_functions.py +++ b/piranha/analysis/phylo_functions.py @@ -193,13 +193,22 @@ def update_local_database(sample_sequences,detailed_csv,new_db_seqs,new_db_metad for record in SeqIO.parse(sample_sequences, "fasta"): new_record = record desc_list = new_record.description.split(" ") - new_desc_list = [i for i in desc_list if not i.startswith("barcode=")] - new_record.description = " ".join(new_desc_list) + write_record = True + + for i in desc_list: + if i.startswith("variant_count"): + count = int(i.split("=")[1]) + if count < 6: + write_record = False - SeqIO.write(new_record, fw, "fasta") - countnew+=1 - sample = record.id.split("|")[0] - record_ids[record.id] = sample + if write_record: + new_desc_list = [i for i in desc_list if not i.startswith("barcode=")] + new_record.description = " ".join(new_desc_list) + + SeqIO.write(new_record, fw, "fasta") + countnew+=1 + sample = record.id.split("|")[0] + record_ids[record.id] = sample with open(new_db_metadata,"w") as fw: with open(detailed_csv,"r") as f: