From c56e7f0bffc4458cc5374eb076810d40198b7b7f Mon Sep 17 00:00:00 2001
From: hjulienn <hanna.julienne@pasteur.fr>
Date: Wed, 18 May 2022 23:00:18 +0200
Subject: [PATCH] test to fix gencov
---
jass/models/worktable.py | 19 +++++++++++++------
1 file changed, 13 insertions(+), 6 deletions(-)
diff --git a/jass/models/worktable.py b/jass/models/worktable.py
index fe0f6a46..05546e14 100644
--- a/jass/models/worktable.py
+++ b/jass/models/worktable.py
@@ -865,11 +865,18 @@ def get_worktable_gencov(project_hdf_path: str):
for i in range(gencov.shape[0]):
for j in range(i, gencov.shape[0]):
- lines.append({
- "phenotypeID_A": sorted_trait.iloc[i],
- "phenotypeID_B": sorted_trait.iloc[j],
- "gencov":gencov.loc[sorted_trait.index[i], sorted_trait.index[j]]
- })
+ if np.isnan(gencov.loc[sorted_trait.index[i], sorted_trait.index[j]]):
+ lines.append({
+ "phenotypeID_A": sorted_trait.iloc[i],
+ "phenotypeID_B": sorted_trait.iloc[j],
+ "gencov":"null"
+ })
+ else:
+ lines.append({
+ "phenotypeID_A": sorted_trait.iloc[i],
+ "phenotypeID_B": sorted_trait.iloc[j],
+ "gencov":gencov.loc[sorted_trait.index[i], sorted_trait.index[j]]
+ })
print(lines)
return lines
@@ -1062,4 +1069,4 @@ def create_genome_full_csv_lock_file(project_hdf_path):
the_lock = "The lock is set on : workTable.csv is not yet available"
file_lock = open(the_lock_path, "w")
file_lock.write(the_lock)
- file_lock.close()
\ No newline at end of file
+ file_lock.close()
--
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