From e5c903a822a9f6ebb0b89abb8ec79d4acafcea4e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 2 Apr 2024 13:47:58 +0200 Subject: [PATCH] reduced id threshold for reference allele evaluation from 0.90 to 0.85 --- taranis/clustering.py | 2 +- taranis/eval_cluster.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/taranis/clustering.py b/taranis/clustering.py index e53fa36..9aea468 100644 --- a/taranis/clustering.py +++ b/taranis/clustering.py @@ -22,7 +22,7 @@ def __init__( ref_seq_name: str, resolution: float = 0.75, seed: int = None, - dist_value: float = 0.9, + dist_value: float = 0.85, ): """ClusterDistance instance creation diff --git a/taranis/eval_cluster.py b/taranis/eval_cluster.py index 2fc2c19..63bbffc 100644 --- a/taranis/eval_cluster.py +++ b/taranis/eval_cluster.py @@ -156,7 +156,7 @@ def evaluate_clusters( query_file.write(">" + r_id + "\n" + r_seq) query_file.seek(0) blast_result = self.blast_obj.run_blast( - query_file.read(), perc_identity=90, query_type="stdin" + query_file.read(), perc_identity=85, query_type="stdin" ) # Close object and discard memory buffer query_file.close()