From f498de920f591b67d333ec821964c9a33ca20096 Mon Sep 17 00:00:00 2001
From: noord087 <ben.noordijk@wur.nl>
Date: Wed, 30 Mar 2022 14:56:44 +0200
Subject: [PATCH] Updated inference procedure of deepnano and guppy to increase
their performance
---
.../compare_accuracy.py | 26 ++++++++++++-------
1 file changed, 17 insertions(+), 9 deletions(-)
diff --git a/compare_benchmark_performance/compare_accuracy.py b/compare_benchmark_performance/compare_accuracy.py
index c9d0978..1e63371 100644
--- a/compare_benchmark_performance/compare_accuracy.py
+++ b/compare_benchmark_performance/compare_accuracy.py
@@ -114,9 +114,18 @@ def parse_paf(paf_path, ground_truth):
y_true = merged_df['species id'].apply(lambda x:
1 if x.find(target_id) == 0
else 0)
- # Mapping to a * means mapping to no species
- y_pred = merged_df['Target sequence name'].apply(
- lambda x: 0 if x == '*' else 1)
+ if tool == 'deepnano':
+ residue_matches = np.array(merged_df["Number of residue matches"])
+ alignment_length = np.array(merged_df["Alignment block length"])
+ align_perc = residue_matches / alignment_length
+ y_pred = (align_perc > 0.50).astype(int)
+ elif tool == 'uncalled':
+ # Mapping to a * means mapping to no species
+ y_pred = merged_df['Target sequence name'].apply(
+ lambda x: 0 if x == '*' else 1)
+ else:
+ raise ValueError('Tool not found')
+
f1 = f1_score(y_true, y_pred)
accuracy = accuracy_score(y_true, y_pred)
cm = confusion_matrix(y_true, y_pred)
@@ -204,8 +213,7 @@ def calculate_accuracy_from_output(args):
"squigglenet/*/fold?/inference")
# Prepare arguments to parse to the functions in the pool
args_baseless = [[file, ground_truth] for file in baseless_files]
- args_uncalled_deepnano = [[file, ground_truth] for file
- in chain(deepnano_files, uncalled_files)]
+ args_uncalled = [[file, ground_truth] for file in uncalled_files]
args_guppy = [[file, ground_truth] for file in guppy_files]
args_squigglenet = [[folder, ground_truth]
for folder in squigglenet_files]
@@ -213,11 +221,11 @@ def calculate_accuracy_from_output(args):
baseless_results = p.starmap(parse_baseless_output, args_baseless)
squigglenet_results = p.starmap(parse_squigglenet_output,
args_squigglenet)
- uncalled_deepnano_results = p.starmap(parse_paf,
- args_uncalled_deepnano)
+ uncalled_results = p.starmap(parse_paf, args_uncalled)
guppy_results = p.starmap(parse_sequencing_summary, args_guppy)
- all_records = (uncalled_deepnano_results + guppy_results
- + squigglenet_results + baseless_results)
+ deepnano_results = [parse_paf(file, ground_truth) for file in deepnano_files]
+ all_records = (guppy_results + deepnano_results + uncalled_results
+ + baseless_results + squigglenet_results)
assert all_records, ('No files found: make sure the input folder '
'contains directories called "uncalled",'
' "guppy", "baseless" and "deepnano"')
--
GitLab