Add saureus validation notebook

notebooks/saureus_notebooks.ipynb

@@ -0,0 +1,129 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Staphylococcus aureus validation\n",
+    "\n",
+    "## Step 1: Import Libraries"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import subprocess\n",
+    "import pandas as pd\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Set input & output filepaths\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "saureus_total_csv_fpath = \"/data/bnf/dev/ryan/pipelines/jasen/validations/saureus/saureus_total.csv\"\n",
+    "saureus_total_sh_fpath = \"/data/bnf/dev/ryan/pipelines/jasen/validations/saureus/saureus_total.csv\"\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Run jasentool validate"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "saureus_validate_cmd = [\n",
+    "    'jasentool', 'validate',\n",
+    "    '--input_dir', '/fs1/results_dev/jasen/saureus/analysis_result/',\n",
+    "    '--db_name', 'cgviz',\n",
+    "    '--db_collection', 'sample',\n",
+    "    '--output_dir', '/data/bnf/dev/ryan/validation/saureus',\n",
+    "    '--combined_output'\n",
+    "]\n",
+    "\n",
+    "# Execute the command\n",
+    "saureus_validate_results = subprocess.run(saureus_validate_cmd, capture_output=True, text=True)\n",
+    "\n",
+    "# Print the outputs\n",
+    "print(\"Saureus validate standard output:\")\n",
+    "print(saureus_validate_results.stdout)\n",
+    "\n",
+    "print(\"Saureus validate standard error:\")\n",
+    "print(saureus_validate_results.stderr)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Run jasentool missing to create a csv of all the samples "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "saureus_missing_cmd = [\n",
+    "    'jasentool', 'missing',\n",
+    "    '--db_name', 'cgviz',\n",
+    "    '--db_collection', 'sample',\n",
+    "    '--analysis_dir', '/fs1/results/jasen/saureus/analysis_result/',\n",
+    "    '--restore_dir', '/fs1/ryan/pipelines/jasen/reruns/seqdata/',\n",
+    "    '--restore_file', saureus_total_sh_fpath,\n",
+    "    '-o', saureus_total_csv_fpath\n",
+    "    ]\n",
+    "\n",
+    "# Execute the command\n",
+    "saureus_missing_results = subprocess.run(saureus_missing_cmd, capture_output=True, text=True)\n",
+    "\n",
+    "# Print the outputs\n",
+    "print(\"Saureus missing standard output:\")\n",
+    "print(saureus_missing_results.stdout)\n",
+    "\n",
+    "print(\"Saureus missing standard error:\")\n",
+    "print(saureus_missing_results.stderr)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "jasentool",
+   "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": "3.12.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}