From 314de17d90525e003eb9ba1e5434f6995da3a5dc Mon Sep 17 00:00:00 2001
From: papanikos <n.pappas@uu.nl>
Date: Thu, 14 Jan 2021 08:40:32 +0100
Subject: [PATCH] fix for pandas warnings
---
workflow/scripts/get_lca.py | 20 ++++++++++++++++----
1 file changed, 16 insertions(+), 4 deletions(-)
diff --git a/workflow/scripts/get_lca.py b/workflow/scripts/get_lca.py
index 3790ebc..4d6a9a8 100644
--- a/workflow/scripts/get_lca.py
+++ b/workflow/scripts/get_lca.py
@@ -142,14 +142,26 @@ if __name__ == '__main__':
index_col='contig'
)
prediction_cols = [c for c in data.columns if c.endswith('_pred')]
+
+ # Slice and make a copy to supress SettingWithCopyWarning
+ hosts = data[prediction_cols].copy()
+ # Set the data type to string so the sanitizing will work
+ for col in prediction_cols:
+ hosts[col] = hosts[col].astype('string')
+
# Sanitize columns to be able to query the taxonomy
- hosts = data[prediction_cols]
if 'vhulk_pred' in prediction_cols:
- hosts['vhulk_pred'] = hosts['vhulk_pred'].str.replace('_', ' ')
+ hosts['vhulk_pred'] = hosts['vhulk_pred'].str.replace('_', ' ')
if 'wish_pred' in prediction_cols:
- hosts['wish_pred'] = [' '.join(i.split(';')[-2].split()[:2])
- for i in data['wish_pred'].values]
+ # Original is superkingdom;kingdom;...;species;name
+ # This selects species
+ hosts['wish_pred'] = hosts['wish_pred'].str.split(';').str.get(-2)
+ # This splits the species and gets the first 2 elements
+ # sometimes species contains strain info two
+ hosts['wish_pred'] = hosts['wish_pred'].str.split().str[:2]
+ # Rejoin the species in a single string `genus species`
+ hosts['wish_pred'] = hosts['wish_pred'].str.join(' ')
hosts = hosts.apply(translate_row)
--
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