Fix resource links in fetchmgs.ipynb example notebook

althonos · Jun 19, 2024 · 04a516b · 04a516b
1 parent 4be5996
commit 04a516b
Showing 1 changed file with 3 additions and 3 deletions.
diff --git 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",