checkpoint before notebook overhaul

workflow/notebooks/2_clock_model.py.ipynb

@@ -0,0 +1,76 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "growing-level",
+   "metadata": {},
+   "source": [
+    "# Objectives\n",
+    "\n",
+    "1. Filter Outlier Tips\n",
+    "1. Estimate a Clock Model"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "senior-russell",
+   "metadata": {},
+   "source": [
+    "# 1. Filter Outlier Tips"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "unavailable-concentrate",
+   "metadata": {},
+   "source": [
+    "## Parse Tip Dates"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "appointed-singer",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Use the utils function to parse the metadata dates\n",
+    "dates_raw = treetime.utils.parse_dates(metadata_path, \n",
+    "                                   date_col=DATE_COL, \n",
+    "                                   name_col = NAME_COL)\n",
+    "\n",
+    "# Remove nan elements (internal nodes)\n",
+    "dates = {}\n",
+    "for k,v in dates_raw.items():\n",
+    "    if type(v) == list:\n",
+    "        dates[k] = v\n",
+    "    elif not pd.isnull(v):\n",
+    "        dates[k] = v\n",
+    "        \n",
+    "# Add Reference\n",
+    "dates[\"Reference\"] = REF_DATE"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.7.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

workflow/notebooks/3_mugration.py.ipynb

@@ -53,7 +53,9 @@
     "\n",
     "import matplotlib.pyplot as plt\n",
     "from matplotlib import colors, lines, patches, gridspec\n",
-    "import seaborn as sns"
+    "import seaborn as sns\n",
+    "\n",
+    "import pickle"
    ]
   },
   {
@@ -1659,6 +1661,13 @@
     "    # Export\n",
     "    out_path = os.path.join(outdir, SCRIPT_NAME + \"_tree_{}.{}\".format(attr.lower(), FMT))  \n",
     "    plt.savefig(out_path, dpi=dpi, bbox_inches = \"tight\")\n",
+    "    \n",
+    "    # Save Tree!\n",
+    "    out_path_pickle_tree = os.path.join(outdir,  SCRIPT_NAME + \"_{}.phylo.obj\".format(attr.lower()))\n",
+    "    with open(out_path_pickle_tree,\"wb\") as outfile:\n",
+    "        dill.dump(tree_div, outfile)\n",
+    "    \n",
+    "    \n",
     "\n",
     "file_colors.close()"
    ]
@@ -1686,7 +1695,11 @@
    "source": [
     "# Save tree dataframe with mugration info\n",
     "out_path_df = os.path.join(outdir, SCRIPT_NAME + \".tsv\" )\n",
-    "tree_df.to_csv(out_path_df, sep=\"\\t\")"
+    "out_path_pickle_df = os.path.join(outdir,  SCRIPT_NAME + \".df.obj\" )\n",
+    "\n",
+    "tree_df.to_csv(out_path_df, sep=\"\\t\")\n",
+    "with open(out_path_pickle_df,\"wb\") as outfile:\n",
+    "    dill.dump(tree_df, outfile)"
    ]
   },
   {