Merge pull request #151 from PyEED/fixes_mutations_docs

Fixes mutations docs

Author: haeussma

docs/usage/embedding_different_models.ipynb

@@ -11,18 +11,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/nab/anaconda3/envs/pyeed_niklas_env/lib/python3.10/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
-      "  from .autonotebook import tqdm as notebook_tqdm\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import sys\n",
     "\n",
@@ -47,15 +38,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "📡 Connected to database.\n",
-      "The provided date does not match the current date. Date is you gave is 2025-03-19 actual date is 2025-04-09\n"
+      "All data has been wiped from the database.\n"
      ]
     }
    ],
@@ -66,7 +57,7 @@
     "\n",
     "eedb = Pyeed(uri, user=user, password=password)\n",
     "\n",
-    "eedb.db.wipe_database(date=\"2025-03-19\")"
+    "eedb.db.wipe_database(date=\"2025-05-16\")"
    ]
   },
   {
@@ -85,7 +76,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -111,21 +102,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
      "data": {
-      "text/html": [
-       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">/home/nab/anaconda3/envs/pyeed_niklas_env/lib/python3.10/site-packages/rich/live.py:231: UserWarning: install \n",
-       "\"ipywidgets\" for Jupyter support\n",
-       "  warnings.warn('install \"ipywidgets\" for Jupyter support')\n",
-       "</pre>\n"
-      ],
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "2dec96f51ab84ce3af3750b48065738d",
+       "version_major": 2,
+       "version_minor": 0
+      },
       "text/plain": [
-       "/home/nab/anaconda3/envs/pyeed_niklas_env/lib/python3.10/site-packages/rich/live.py:231: UserWarning: install \n",
-       "\"ipywidgets\" for Jupyter support\n",
-       "  warnings.warn('install \"ipywidgets\" for Jupyter support')\n"
+       "Output()"
       ]
      },
      "metadata": {},
@@ -135,8 +123,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Region ids: [5206, 5205, 5203, 5201, 5207]\n",
-      "len of ids: 5\n"
+      "Region ids: [849, 843, 848, 842, 847, 841, 846, 839, 850, 844]\n",
+      "len of ids: 5\n",
+      "Number of existing pairs: 0\n",
+      "Number of total pairs: 4\n",
+      "Number of pairs to align: 4\n"
      ]
     },
     {
@@ -200,7 +191,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -217,7 +208,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -253,14 +244,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "{'from_positions': [272, 241, 125], 'to_positions': [272, 241, 125], 'from_monomers': ['D', 'R', 'V'], 'to_monomers': ['N', 'S', 'I']}\n"
+      "{'from_positions': [241, 272, 125], 'to_positions': [241, 272, 125], 'from_monomers': ['R', 'D', 'V'], 'to_monomers': ['S', 'N', 'I']}\n"
      ]
     }
    ],
@@ -298,21 +289,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Mutation on position 17 -> 17 with a nucleotide change of T -> C\n",
-      "Mutation on position 395 -> 395 with a nucleotide change of T -> G\n",
-      "Mutation on position 198 -> 198 with a nucleotide change of C -> A\n",
-      "Mutation on position 716 -> 716 with a nucleotide change of G -> A\n",
-      "Mutation on position 705 -> 705 with a nucleotide change of G -> A\n",
-      "Mutation on position 473 -> 473 with a nucleotide change of T -> C\n",
-      "Mutation on position 720 -> 720 with a nucleotide change of A -> C\n",
-      "Mutation on position 137 -> 137 with a nucleotide change of A -> G\n"
+      "Mutation on position 474 -> 474 with a nucleotide change of T -> C\n",
+      "Mutation on position 199 -> 199 with a nucleotide change of C -> A\n",
+      "Mutation on position 138 -> 138 with a nucleotide change of A -> G\n",
+      "Mutation on position 18 -> 18 with a nucleotide change of T -> C\n",
+      "Mutation on position 396 -> 396 with a nucleotide change of T -> G\n",
+      "Mutation on position 721 -> 721 with a nucleotide change of A -> C\n",
+      "Mutation on position 706 -> 706 with a nucleotide change of G -> A\n",
+      "Mutation on position 717 -> 717 with a nucleotide change of G -> A\n"
      ]
     }
    ],
@@ -323,6 +314,13 @@
     "    )"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,

docs/usage/embeddings_analysis.ipynb

@@ -40,6 +40,9 @@ crc64iso = "0.0.2"
 SPARQLWrapper = "2.0.0"
 pysam = "0.23.0"
 types-requests = "2.32.0.20250328"
+ipywidgets = "^8.1.7"
+sentencepiece = "^0.2.0"
+umap = "^0.1.1"
 
 [tool.poetry.group.dev.dependencies]
 mkdocstrings = {extras = ["python"], version = "^0.26.2"}