update documentation and re-order args

IoannaNika · Dec 24, 2024 · 6536eba · 6536eba
1 parent db46507
commit 6536eba
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/src/benchmarking_scripts/evaluate_hrt_output_lumc.py b/src/benchmarking_scripts/evaluate_hrt_output_lumc.py
@@ -401,7 +401,7 @@ def main():
     recalls = [recall_wuhan, recall_omicron]
     recalls = [x for x in recalls if str(x) != 'nan']
     recall = round(sum(recalls)/len(recalls),3)
-    precision_omicron, precision_wuhan = calculate_precision(number_of_all_haplotypes_per_region = number_of_all_haplotypes_per_region,number_of_assigned_haplotypes_per_region = number_of_haplotypes_per_region)
+    precision_omicron, precision_wuhan = calculate_precision(number_of_assigned_haplotypes_per_region = number_of_haplotypes_per_region, number_of_all_haplotypes_per_region = number_of_all_haplotypes_per_region)
     precisions = [precision_omicron, precision_wuhan]
     precisions = [x for x in precisions if str(x) != 'nan']
     precision = round(sum(precisions)/len(precisions),3)

diff --git a/src/utils/evaluation.py b/src/utils/evaluation.py
@@ -106,8 +106,8 @@ def calculate_precision(number_of_assigned_haplotypes_per_region:dict, number_of
     Calculates the precision for Wuhan and Omicron haplotypes. How many of the reconstructed haplotypes assigned to Wuhan and Omicron are exact matches to the true haplotypes?
 
     Args:
-    number_of_exact_haplotypes_per_region: dict, number of exact haplotypes per region dictionary
-    number_of_haplotypes_per_region: dict, number of haplotypes per region dictionary
+    number_of_assigned_haplotypes_per_region: dict, number of haplotypes assigned to Wuhan or Omicron per region (not discarded)
+    number_of_all_haplotypes_per_region: dict, number of all reconstructed haplotypes per region
 
     Returns:
     precision_wuhan: float, precision for Wuhan haplotypes