From ae8116bf9f7734571cc30602a50aad30eb6acd65 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Fri, 28 Oct 2022 14:25:45 +0200
Subject: [PATCH] Escaping column name in query.
This caused bugs with libraries named "1_1", which was interpreted as
number 11.
---
RNA_Seq_Cecere/RNA-seq.snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index 03798aa..fd6421f 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -1367,10 +1367,10 @@ def do_linear_regression(data, x_col, y_col, y_min=0, fit_intercept=True, transf
"""
if transform is not None:
data = getattr(np, transform)(
- data[[x_col, y_col]].dropna().query(f"{y_col} >= {y_min}")).replace(
+ data[[x_col, y_col]].dropna().query(f"`{y_col}` >= {y_min}")).replace(
[np.inf, -np.inf], np.nan).dropna()
else:
- data = data[[x_col, y_col]].dropna().query(f"{y_col} >= {y_min}")
+ data = data[[x_col, y_col]].dropna().query(f"`{y_col}` >= {y_min}")
lm = LinearRegression(fit_intercept=fit_intercept)
X = data.drop(y_col, axis=1)
lm.fit(X, data[y_col])
--
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