From 6ceb75049893b95e93e2a8cb7a76e7d92bc32afd Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Fri, 28 Oct 2022 11:36:53 +0200
Subject: [PATCH] Catching more errors due to bad data.
---
RNA_Seq_Cecere/RNA-seq.snakefile | 11 +++++------
1 file changed, 5 insertions(+), 6 deletions(-)
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index 663e409..165feb9 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -139,6 +139,10 @@ from smwrappers import wrappers_dir
NO_DATA_ERRS = [
"Empty 'DataFrame': no numeric data to plot",
"no numeric data to plot"]
+BAD_DATA_ERRS = [
+ "`dataset` input should have multiple elements.",
+ "array must not contain infs or NaNs",
+ "zero-size array to reduction operation fmax which has no identity"]
alignment_settings = {"bowtie2": "", "hisat2": "", "crac": "-k 20 --stranded --use-x-in-cigar"}
@@ -1673,12 +1677,7 @@ rule test_size_factor:
else:
raise
except ValueError as e:
- if str(e) == "`dataset` input should have multiple elements.":
- warn("\n".join([
- "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":
+ if str(e) in BAD_DATA_ERRS:
warn("\n".join([
"Got ValueError:", f"{str(e)}",
f"Data cannot be plotted for {normalizer}",
--
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