From 30b35d319ade79664714dfe82517f02e01739d43 Mon Sep 17 00:00:00 2001
From: noord087 <ben.noordijk@wur.nl>
Date: Wed, 30 Mar 2022 14:56:33 +0200
Subject: [PATCH] Now use 95% alignment cutoff for guppy
---
compare_benchmark_performance/compare_accuracy.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/compare_benchmark_performance/compare_accuracy.py b/compare_benchmark_performance/compare_accuracy.py
index fe91bb7..c9d0978 100644
--- a/compare_benchmark_performance/compare_accuracy.py
+++ b/compare_benchmark_performance/compare_accuracy.py
@@ -68,7 +68,7 @@ def parse_sequencing_summary(file_path, ground_truth):
1 if x.find(target_id) == 0
else 0)
- y_pred = df['alignment_genome'].apply(lambda x: 0 if x == '*' else 1)
+ y_pred = df['alignment_identity'].apply(lambda x: 0 if x < 0.95 else 1)
f1 = f1_score(y_true, y_pred)
accuracy = accuracy_score(y_true, y_pred)
cm = confusion_matrix(y_true, y_pred)
--
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