From 953cc2980d0bb81ceace7cbd8b28e1ec707146c9 Mon Sep 17 00:00:00 2001 From: Amine GHOZLANE Date: Tue, 14 Jan 2025 22:40:20 +0100 Subject: [PATCH] Increase similarity threshold for fast mode --- meteor/counter.py | 3 +-- meteor/session.py | 1 - 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/meteor/counter.py b/meteor/counter.py index 57ba37f..4779d18 100644 --- a/meteor/counter.py +++ b/meteor/counter.py @@ -16,7 +16,6 @@ import sys import pysam import lzma -import pandas as pd from dataclasses import dataclass, field from tempfile import mkdtemp, mkstemp from pathlib import Path @@ -38,7 +37,7 @@ class Counter(Session): DEFAULT_COUNTING_TYPE: ClassVar[str] = "smart_shared" NO_IDENTITY_THRESHOLD: ClassVar[float] = 0.0 DEFAULT_IDENTITY_THRESHOLD_COMPLETE: ClassVar[float] = 0.95 - DEFAULT_IDENTITY_THRESHOLD_TAXO: ClassVar[float] = 0.97 + DEFAULT_IDENTITY_THRESHOLD_TAXO: ClassVar[float] = 0.98 meteor: type[Component] counting_type: str diff --git a/meteor/session.py b/meteor/session.py index 8f4cd1d..27b8322 100644 --- a/meteor/session.py +++ b/meteor/session.py @@ -30,7 +30,6 @@ class Component: MIN_BOWTIE2_VERSION: ClassVar[Version] = Version("2.3.5") MIN_FREEBAYES_VERSION: ClassVar[Version] = Version("1.3.6") - # MIN_MAFFT_VERSION: ClassVar[Version] = Version("7.487") DEFAULT_GAP_CHAR: ClassVar[str] = "N" DEFAULT_CORE_SIZE: ClassVar[int] = 100