Updated metabolic data to include info from Human1 GEM too.

earmingol · Jul 12, 2024 · 0977ea1 · 0977ea1
1 parent f681cde
commit 0977ea1
Show file tree

Hide file tree

Showing 4 changed files with 3,061 additions and 897 deletions.
diff --git a/task_data/Generate-Human-from-MATLAB.ipynb b/task_data/Generate-Human-from-MATLAB.ipynb
@@ -2503,7 +2503,7 @@
        "  </thead>\n",
        "  <tbody>\n",
        "    <tr>\n",
-       "      <th>85</th>\n",
+       "      <th>130</th>\n",
        "      <td>5689</td>\n",
        "      <td>9537</td>\n",
        "      <td>[HC5, NEDMHAL, PMSB1, PSC5]</td>\n",
@@ -2517,11 +2517,11 @@
        "</div>"
       ],
       "text/plain": [
-       "   query  HGNC                        alias entrezgene  \\\n",
-       "85  5689  9537  [HC5, NEDMHAL, PMSB1, PSC5]       5689   \n",
+       "    query  HGNC                        alias entrezgene  \\\n",
+       "130  5689  9537  [HC5, NEDMHAL, PMSB1, PSC5]       5689   \n",
        "\n",
-       "                             name symbol  taxid  \n",
-       "85  proteasome 20S subunit beta 1  PSMB1   9606  "
+       "                              name symbol  taxid  \n",
+       "130  proteasome 20S subunit beta 1  PSMB1   9606  "
       ]
      },
      "execution_count": 38,
@@ -2958,7 +2958,7 @@
    },
    "outputs": [],
    "source": [
-    "metabolic_genes = list(set(rxn_gene_df.Gene.unique()))"
+    "metabolic_genes = sorted(set(rxn_gene_df.Gene.unique()))"
    ]
   },
   {
@@ -4301,7 +4301,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 90,
+   "execution_count": 87,
    "id": "1f389626-4f10-414a-b2d9-30e150d33dcf",
    "metadata": {
     "tags": []
@@ -4314,19 +4314,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 91,
+   "execution_count": 88,
    "id": "da225683-1a4f-44a0-be21-95c3df39a037",
    "metadata": {
     "tags": []
    },
    "outputs": [],
    "source": [
-    "all_met_genes = list(set(metabolic_genes + human1_genes))"
+    "all_met_genes = sorted(set(metabolic_genes + human1_genes))"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 93,
+   "execution_count": 89,
    "id": "81e2ee0b-e361-4f1f-9648-590fee7cb6c9",
    "metadata": {
     "tags": []