save timetrees and divtrees for all relevant methods

ktmeaton · Feb 26, 2021 · 7ea625a · 7ea625a
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diff --git a/docs/notes/Notes_Development.md b/docs/notes/Notes_Development.md
@@ -1,4 +1,4 @@
 # Development
 
 1. Update coord_x and coord_y in clock_model.
-1. Save an output divergence tree from clock_model.
+1. Save timetrees and divtrees for all relevant methods.
diff --git a/results/clock_model/clock_model_divtree.nexus b/results/clock_model/clock_model_divtree.nexus
diff --git a/results/clock_model/clock_model_divtree.xml b/results/clock_model/clock_model_divtree.xml
diff --git a/results/clock_model/clock_model.nexus → ...ts/clock_model/clock_model_timetree.nexus b/results/clock_model/clock_model.nexus → ...ts/clock_model/clock_model_timetree.nexus
diff --git a/results/clock_model/clock_model.nwk → results/clock_model/clock_model_timetree.nwk b/results/clock_model/clock_model.nwk → results/clock_model/clock_model_timetree.nwk
diff --git a/results/clock_model/clock_model.xml → results/clock_model/clock_model_timetree.xml b/results/clock_model/clock_model.xml → results/clock_model/clock_model_timetree.xml
diff --git a/workflow/notebooks/2_clock_model.py.ipynb b/workflow/notebooks/2_clock_model.py.ipynb
@@ -3867,26 +3867,18 @@
   },
   {
    "cell_type": "markdown",
-   "id": "defined-sculpture",
+   "id": "sitting-saying",
    "metadata": {},
    "source": [
     "## Divergence coord_x and coord_y"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 60,
-   "id": "lasting-realtor",
+   "execution_count": 64,
+   "id": "honest-rendering",
    "metadata": {},
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "DEPRECATED: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.\n",
-      "\n"
-     ]
-    },
     {
      "data": {
       "text/html": [
@@ -4552,7 +4544,7 @@
        "[1065 rows x 34 columns]"
       ]
      },
-     "execution_count": 60,
+     "execution_count": 64,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -4589,10 +4581,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 65,
    "id": "overhead-extent",
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "DEPRECATED: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.\n",
+      "\n"
+     ]
+    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -4659,10 +4659,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 57,
+   "execution_count": 66,
    "id": "scheduled-chambers",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "DEPRECATED: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "metadata_to_comment(tt.tree, tree_df)"
    ]
@@ -4681,13 +4690,46 @@
    "id": "thousand-austin",
    "metadata": {},
    "source": [
-    "## Dataframe and Trees"
+    "## Dataframe"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 58,
-   "id": "foster-works",
+   "execution_count": 71,
+   "id": "precious-webmaster",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "DEPRECATED: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Dataframe\n",
+    "out_path_df = os.path.join(outdir, SCRIPT_NAME + \".tsv\" )\n",
+    "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)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "liberal-observer",
+   "metadata": {},
+   "source": [
+    "## Timetrees"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 74,
+   "id": "residential-faith",
    "metadata": {},
    "outputs": [
     {
@@ -4696,46 +4738,80 @@
        "1"
       ]
      },
-     "execution_count": 58,
+     "execution_count": 74,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "# Dataframe\n",
-    "out_path_df = os.path.join(outdir, SCRIPT_NAME + \".tsv\" )\n",
-    "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)\n",
-    "\n",
     "# Phyloxml\n",
-    "out_path_xml = os.path.join(outdir,  SCRIPT_NAME + \".xml\" )\n",
-    "Phylo.write(tt.tree, out_path_xml, 'phyloxml')\n",
+    "tt_copy = copy.deepcopy(tt)\n",
+    "out_path_xml = os.path.join(outdir,  SCRIPT_NAME + \"_timetree.xml\" )\n",
+    "Phylo.write(tt_copy.tree, out_path_xml, 'phyloxml')\n",
     "\n",
     "# Nexus\n",
-    "out_path_nexus = os.path.join(outdir, SCRIPT_NAME + \".nexus\" )\n",
-    "Phylo.write(tt.tree, out_path_nexus, 'nexus', format_branch_length='%1.{}f'.format(BRANCH_LEN_SIG_DIG))\n",
+    "out_path_nexus = os.path.join(outdir, SCRIPT_NAME + \"_timetree.nexus\" )\n",
+    "Phylo.write(tt_copy.tree, out_path_nexus, 'nexus', format_branch_length='%1.{}f'.format(BRANCH_LEN_SIG_DIG))\n",
     "\n",
     "# Dill object\n",
-    "out_path_dill_tree = os.path.join(outdir,  SCRIPT_NAME + \".treetime.obj\" )\n",
+    "out_path_dill_tree = os.path.join(outdir,  SCRIPT_NAME + \"_timetree.treetime.obj\" )\n",
     "with open(out_path_dill_tree,\"wb\") as outfile:\n",
-    "    dill.dump(tt, outfile)\n",
+    "    dill.dump(tt_copy, outfile)\n",
     "    \n",
     "# Newick (remove comments)\n",
-    "tt_copy = copy.deepcopy(tt)\n",
     "for c in tt_copy.tree.find_clades(): c.comment = None\n",
-    "    \n",
-    "# Newick Timetree\n",
-    "out_path_nwk = os.path.join(outdir, SCRIPT_NAME + \".nwk\" )\n",
-    "Phylo.write(tt_copy.tree, out_path_nwk, 'newick', format_branch_length='%1.{}f'.format(BRANCH_LEN_SIG_DIG))\n",
-    "\n",
-    "# Newick Divergence\n",
+    "out_path_nwk = os.path.join(outdir, SCRIPT_NAME + \"_timetree.nwk\" )\n",
+    "Phylo.write(tt_copy.tree, out_path_nwk, 'newick', format_branch_length='%1.{}f'.format(BRANCH_LEN_SIG_DIG))\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "continuing-thong",
+   "metadata": {},
+   "source": [
+    "## Divtrees"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 75,
+   "id": "foster-works",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1"
+      ]
+     },
+     "execution_count": 75,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "tt_copy = copy.deepcopy(tt)\n",
+    "# Convert to divtree\n",
     "for n in tt_copy.tree.find_clades():\n",
     "    n.branch_length=n.mutation_length\n",
-    "out_path_div_nwk = os.path.join(outdir, SCRIPT_NAME + \"_divtree.nwk\" )\n",
-    "Phylo.write(tt_copy.tree, out_path_div_nwk, 'newick', format_branch_length='%1.{}f'.format(BRANCH_LEN_SIG_DIG))"
+    "\n",
+    "# Phyloxml\n",
+    "out_path_xml = os.path.join(outdir,  SCRIPT_NAME + \"_divtree.xml\" )\n",
+    "Phylo.write(tt_copy.tree, out_path_xml, 'phyloxml')\n",
+    "\n",
+    "# Nexus\n",
+    "out_path_nexus = os.path.join(outdir, SCRIPT_NAME + \"_divtree.nexus\" )\n",
+    "Phylo.write(tt_copy.tree, out_path_nexus, 'nexus', format_branch_length='%1.{}f'.format(BRANCH_LEN_SIG_DIG))\n",
+    "\n",
+    "# Dill object\n",
+    "out_path_dill_tree = os.path.join(outdir,  SCRIPT_NAME + \"_divtree.treetime.obj\" )\n",
+    "with open(out_path_dill_tree,\"wb\") as outfile:\n",
+    "    dill.dump(tt_copy, outfile)\n",
+    "    \n",
+    "# Newick (remove comments)\n",
+    "for c in tt_copy.tree.find_clades(): c.comment = None\n",
+    "out_path_nwk = os.path.join(outdir, SCRIPT_NAME + \"_divtree.nwk\" )\n",
+    "Phylo.write(tt_copy.tree, out_path_nwk, 'newick', format_branch_length='%1.{}f'.format(BRANCH_LEN_SIG_DIG))"
    ]
   },
   {
@@ -4748,19 +4824,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 51,
+   "execution_count": 68,
    "id": "proper-hollow",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "DEPRECATED: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.\n",
-      "\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import importlib\n",
     "import sys\n",
@@ -4770,7 +4837,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 52,
+   "execution_count": 69,
    "id": "structural-amount",
    "metadata": {},
    "outputs": [
@@ -4816,7 +4883,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 53,
+   "execution_count": 70,
    "id": "recent-silicon",
    "metadata": {},
    "outputs": [