From c22ad3fd3690941a9f34da076854e5767eb359ae Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Mon, 11 Jan 2021 16:56:39 +0100
Subject: [PATCH] src/visu/figure_maker.py: add a warning message if some bed
feature cannot be reported
---
src/visu/figure_maker.py | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/src/visu/figure_maker.py b/src/visu/figure_maker.py
index 4599eca..d8bfd7c 100644
--- a/src/visu/figure_maker.py
+++ b/src/visu/figure_maker.py
@@ -15,6 +15,7 @@ import pyBigWig as pbw
import seaborn as sns
import matplotlib.pyplot as plt
from tqdm import tqdm
+from loguru import logger
def load_bed(bed: Path, bed_name: str) -> List[List[Union[int, str]]]:
@@ -111,6 +112,10 @@ def inspect_bigwig_regions(bw: Any, region: List,
3 2.00 3 cond1 R1 exon2
4 2.00 4 cond1 R1 exon2
"""
+ r_start = max(region[1], 0)
+ r_end = min(region[2], bw.chroms(region[0]))
+ if r_end - r_start < nb_bin:
+ return pd.DataFrame()
val = bw.stats(region[0],
max(region[1], 0),
min(region[2], bw.chroms(region[0])),
@@ -173,6 +178,10 @@ def create_sample_table(bw_file: Path, regions: List[List],
for region in tqdm(regions, desc="scanning coverage ..."):
list_df.append(inspect_bigwig_regions(bw, region, replicate, nb_bin,
resize, condition_name))
+ r = sum([df.empty for df in list_df])
+ if r > 0:
+ logger.warning(f"They were {r} bed feature that could not be reported "
+ f"because of their small size")
return pd.concat(list_df, axis=0, ignore_index=True)
--
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