Merge pull request #147 from monarch-initiative/NBAS

Nbas

notebooks/NBAS/NBAS_SOPH_individuals.ipynb

@@ -0,0 +1,123 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# NBAS\n",
+    "[Short stature, optic nerve atrophy, and Pelger-Huet anomaly (SOPH syndrome)](https://www.omim.org/entry/614800) is caused by homozygous mutation in the NBAS gene.\n",
+    "We note that a \"hybrid\" phenotype (combination of features from Infantile liver failure syndrome-2 (ILFS2) and SOPH syndrome) was postulated by\n",
+    "[Staufner C, et al. (2020)](https://pubmed.ncbi.nlm.nih.gov/31761904/). We have coded individuals with acute liver failure together with features of SOPH (such as Pelger Huet anomaly or facial dysmorphism) as SOPH, and included individuals as ILFS2 if the others refer to the corresponding OMIM code or the presentation includes only features of ILFS2."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Using pyphetools version 0.9.100\n"
+     ]
+    }
+   ],
+   "source": [
+    "from pyphetools.creation import TemplateImporter, Moi\n",
+    "from pyphetools.visualization import IndividualTable, QcVisualizer\n",
+    "from IPython.display import display, HTML\n",
+    "import pyphetools\n",
+    "print(f\"Using pyphetools version {pyphetools.__version__}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "HPO version 2024-08-13\n",
+      "Created encoders for 126 fields\n",
+      "Importing OMIM:614800, Short stature, optic nerve atrophy, and Pelger-Huet anomaly, HGNC:15625, NBAS,  NM_015909.4\n",
+      "We output 6 GA4GH phenopackets to the directory phenopackets\n"
+     ]
+    }
+   ],
+   "source": [
+    "template = \"input/NBAS_SOPH_individuals.xlsx\"\n",
+    "created_by = \"0000-0002-0736-9199\"\n",
+    "timporter = TemplateImporter(template=template,  created_by=created_by)\n",
+    "individual_list, cvalidator = timporter.import_phenopackets_from_template()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<h2>Cohort validation</h2>\n",
+       "<p>Errors found with 3 of 6 phenopackets.</p>\n",
+       "<table style=\"border: 2px solid black; align: \"left\">\n",
+       "<caption>Error counts</caption>\n",
+       "<tr><th style=\"text-align: left;font-weight: bold;\">Level</th><th style=\"text-align: left;font-weight: bold;\">Error category</th><th style=\"text-align: left;font-weight: bold;\">Count</th></tr>\n",
+       "<tr><td style=\"text-align: left;\">WARNING</td><td style=\"text-align: left;\">REDUNDANT</td><td style=\"text-align: left;\">5</td></tr>\n",
+       "</table>\n",
+       "<p>A total of 5 issues were fixed and no individual was removed from the cohort.</p>"
+      ],
+      "text/plain": [
+       "<IPython.core.display.HTML object>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "qc = QcVisualizer(cohort_validator=cvalidator)\n",
+    "display(HTML(qc.to_summary_html()))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "ps24venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}