From 4dcf79b45ef28f1235693ee8282e4ee6bfd97695 Mon Sep 17 00:00:00 2001
From: kdc715 <kedic@LIT-PF3VB193.localdomain>
Date: Mon, 27 Jan 2025 17:11:53 +0100
Subject: [PATCH] remove chromosome info from coverage analysis, only keep
contigs
---
.../notebooks/contig_coverage_heatmap.py.ipynb | 18 ++++++++++++++----
1 file changed, 14 insertions(+), 4 deletions(-)
diff --git a/snakemodules/notebooks/contig_coverage_heatmap.py.ipynb b/snakemodules/notebooks/contig_coverage_heatmap.py.ipynb
index 03bd1b5..4a813c2 100644
--- a/snakemodules/notebooks/contig_coverage_heatmap.py.ipynb
+++ b/snakemodules/notebooks/contig_coverage_heatmap.py.ipynb
@@ -160,13 +160,23 @@
},
{
"cell_type": "code",
- "execution_count": 91,
+ "execution_count": null,
"id": "36f31bc9-8eaa-434a-9a81-6a97282fe469",
"metadata": {},
"outputs": [],
"source": [
"coverage_df.rename(columns={'#rname': 'contigs'}, inplace=True)\n",
- "coverage_df.set_index('contigs', inplace=True)\n",
+ "coverage_df.set_index('contigs', inplace=True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "345e2ab4",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "coverage_df = coverage_df[coverage_df.index.str.startswith(\"contig_\")]\n",
"coverage_df = coverage_df.reindex(order_by_length)"
]
},
@@ -217,7 +227,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3 (ipykernel)",
+ "display_name": "base",
"language": "python",
"name": "python3"
},
@@ -231,7 +241,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.10.12"
+ "version": "3.9.12"
}
},
"nbformat": 4,
--
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