From 807bf3f0dadafd35b05ac1429748d3a959ba9ca2 Mon Sep 17 00:00:00 2001
From: Swastik Mishra <swastik.mishra@hhu.de>
Date: Wed, 25 Dec 2024 00:09:32 +0000
Subject: [PATCH] Update readme
---
README.md | 2 ++
notebooks/01-01_download_data.ipynb | 14 +++++++-------
2 files changed, 9 insertions(+), 7 deletions(-)
diff --git a/README.md b/README.md
index 114d5df..a8f6acd 100644
--- a/README.md
+++ b/README.md
@@ -20,3 +20,5 @@ The only other file you need to install is `xlsx2csv` using `pip`:
```
pip install xlsx2csv
```
+
+Additionally, I used `ripgrep` instead of `grep` for faster extraction of subset data from EggNOG. In case you rely on `grep` make edits accordingly in the notebooks (replace commands of `rg`)
diff --git a/notebooks/01-01_download_data.ipynb b/notebooks/01-01_download_data.ipynb
index 265a725..9e6f784 100644
--- a/notebooks/01-01_download_data.ipynb
+++ b/notebooks/01-01_download_data.ipynb
@@ -9,8 +9,10 @@
]
},
{
- "cell_type": "raw",
+ "cell_type": "code",
+ "execution_count": null,
"metadata": {},
+ "outputs": [],
"source": [
"e6_url = \"http://eggnog6.embl.de/download/eggnog_6.0/\"\n",
"all_trees_path = e6_url + \"e6.all_raw_trees_and_algs.tsv\"\n",
@@ -38,12 +40,10 @@
]
},
{
- "cell_type": "raw",
- "metadata": {
- "vscode": {
- "languageId": "raw"
- }
- },
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"%%bash -s \"$data_dir\" \"$all_trees_path\" \"$og2seqs_species_path\" \"$seq2ogs_path\" \"$gold_url\"\n",
"pip install xlsx2csv\n",
--
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