From f3ba3c72e456fc01cb1d0a742548e6ccc4b61114 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Thu, 27 Oct 2022 15:30:21 +0200
Subject: [PATCH] Caught one more exception.
Could happen with columns containing only zero counts.
---
.gitmodules | 2 +-
RNA_Seq_Cecere/RNA-seq.snakefile | 5 +++++
2 files changed, 6 insertions(+), 1 deletion(-)
diff --git a/.gitmodules b/.gitmodules
index ac0bbc4..b381cff 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -42,4 +42,4 @@
url = git@gitlab.pasteur.fr:bli/gtf2attr.git
[submodule "libbamutils"]
path = libbamutils
- url = https://gitlab.pasteur.fr/bli/libbamutils.git
+ url = git@gitlab.pasteur.fr:bli/libbamutils.git
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index 429e66a..663e409 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -1678,6 +1678,11 @@ rule test_size_factor:
"Got ValueError:", f"{str(e)}",
f"Data cannot be plotted for {normalizer}",
f"{data}\n"]))
+ elif str(e) == "array must not contain infs or NaNs":
+ warn("\n".join([
+ "Got ValueError:", f"{str(e)}",
+ f"Data cannot be plotted for {normalizer}",
+ f"{data}\n"]))
else:
raise
# xlabel = "log10(normalized counts)"
--
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