From a763c9a0766c05b9ae80da5f18b59afe2c02b691 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Thu, 24 Sep 2020 09:45:09 +0200
Subject: [PATCH] Catch stats numeric error.
---
libhts/libhts.py | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/libhts/libhts.py b/libhts/libhts.py
index bb4cdda..a68c2d6 100644
--- a/libhts/libhts.py
+++ b/libhts/libhts.py
@@ -456,7 +456,17 @@ def size_factor_correlations(counts_data, summaries, normalizer):
# by_norm = counts_data / size_factors
def compute_pearsonr_with_size_factor(row):
- return pearsonr(row, size_factors)[0]
+ try:
+ return pearsonr(row, size_factors)[0]
+ except ValueError as err:
+ if str(err) == "array must not contain infs or NaNs":
+ msg = (
+ f"Cannot compute Pearson correlation with size factors "
+ f"when normalizing using {normaliser}")
+ warnings.warn(msg)
+ return np.nan
+ else:
+ raise
# return by_norm.apply(compute_pearsonr_with_size_factor, axis=1)
return (counts_data / size_factors).apply(compute_pearsonr_with_size_factor, axis=1)
--
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