From 04a516b18584a6376df7e82dc9e41c97647ad4d0 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Wed, 19 Jun 2024 16:49:34 +0200
Subject: [PATCH] Fix resource links in `fetchmgs.ipynb` example notebook
---
docs/examples/fetchmgs.ipynb | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/docs/examples/fetchmgs.ipynb b/docs/examples/fetchmgs.ipynb
index 0fdc1841..e8df382e 100644
--- a/docs/examples/fetchmgs.ipynb
+++ b/docs/examples/fetchmgs.ipynb
@@ -13,7 +13,7 @@
"id": "094d9734",
"metadata": {},
"source": [
- "This example is adapted from the [fetchMGs](https://github.com/motu-tool/fetchMGs/blob/master/fetchMGs.pl) Perl script used in [mOTU](https://motu-tool.org/) to extract the 40 single-copy universal marker genes from a genome, annotating proteins to find the highest scoring proteins mapping to each of these marker genes.\n",
+ "This example is adapted from the [fetchMGs](https://github.com/motu-tool/fetchMGs/) Perl script used in [mOTU](https://motu-tool.org/) to extract the 40 single-copy universal marker genes from a genome, annotating proteins to find the highest scoring proteins mapping to each of these marker genes.\n",
"\n",
"In this notebook, we show how to reproduce this kind of analysis, using `pyhmmer` instead of HMMER3 to perform the alignments and extract the bit scores.\n",
"\n",
@@ -59,7 +59,7 @@
"import io\n",
"import urllib.request\n",
"\n",
- "url = \"https://github.com/motu-tool/fetchMGs/raw/master/lib/MG_BitScoreCutoffs.allhits.txt\"\n",
+ "url = \"https://github.com/motu-tool/FetchMGs/raw/1.3/fetchmgs/data/MG_BitScoreCutoffs.allhits.txt\"\n",
"\n",
"cutoffs = {}\n",
"with urllib.request.urlopen(url) as f:\n",
@@ -88,7 +88,7 @@
"import urllib.request\n",
"import pyhmmer.plan7\n",
"\n",
- "baseurl = \"https://github.com/motu-tool/fetchMGs/raw/master/lib/{}.hmm\"\n",
+ "baseurl = \"https://github.com/motu-tool/FetchMGs/raw/1.3/fetchmgs/data/{}.hmm\"\n",
"\n",
"hmms = []\n",
"for cog in cutoffs:\n",
--
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