nb/02-building_gene_phylogenies/02-parse_and_store_all_phylogenies.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Loading Phylogenies as ETE PhyloTree instances\n",
    "\n",
    "Once all trees are computed, we want to start analyzing them. Let's first load them as Python objects. \n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**TASK**: Read all trees and load them into a dictionary. Store the dictionary `all_trees` as a pickle file (`data/alltrees.pkl`) \n",
    "\n",
    "Tips:\n",
    "- Use PhyloTree instances and provide a species name parser\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Trees loaded: 2605\n"
     ]
    }
   ],
   "source": [
    "# Read all trees and load them into a dictionary. Store the dictionary 'all_trees' as pickle file (data/alltrees.pkl) \n",
    "import pickle\n",
    "import os\n",
    "from ete3 import PhyloTree\n",
    "\n",
    "def extract_spcode(nodename):\n",
    "    return nodename.split('.')[0]\n",
    "\n",
    "# Load all trees\n",
    "all_trees = {}\n",
    "for basename in open(\"data/target_families.txt\"):\n",
    "    basename = basename.strip()\n",
    "    tree_file = 'data/phylo/%s/mafft_default-none-none-fasttree_default/%s.faa.final_tree.nw' %(basename, basename)\n",
    "    if os.path.exists(tree_file):\n",
    "        t = PhyloTree(tree_file, sp_naming_function=extract_spcode)\n",
    "        all_trees[basename] = t\n",
    "        \n",
    "print(\"Trees loaded:\", len(all_trees))\n",
    "\n",
    "with open('data/alltrees.pkl', 'wb') as ALLTREES:\n",
    "    pickle.dump(all_trees, ALLTREES)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Tip:** To load all trees back in other notebooks, you can now do it like this: "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Trees loaded: 2605\n"
     ]
    }
   ],
   "source": [
    "import pickle\n",
    "def extract_spcode(nodename):\n",
    "    return nodename.split('.')[0]\n",
    "\n",
    "all_trees = pickle.load(open('data/alltrees.pkl', 'rb'))\n",
    "print(\"Trees loaded:\", len(all_trees))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Let's try some Basic tree operations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "We can quickly print it:\n",
      "\n",
      "      /-525897.Dbac_2405\n",
      "   /-|\n",
      "  |   \\-555778.Hneap_1768\n",
      "--|\n",
      "  |      /-637389.Acaty_c1916\n",
      "  |   /-|\n",
      "   \\-|   \\-637389.Acaty_c1239\n",
      "     |\n",
      "      \\-1158165.KB898877_gene1259\n",
      "\n",
      "Get the list of species and sequences included:\n",
      "  Species in tree: {'637389', '525897', '555778', '1158165'}\n",
      "  Seqs in tree: ['525897.Dbac_2405', '555778.Hneap_1768', '637389.Acaty_c1916', '637389.Acaty_c1239', '1158165.KB898877_gene1259']\n",
      "\n",
      "Find nodes by name and read attributes:\n",
      "           Name: 1158165.KB898877_gene1259\n",
      "        Species: 1158165\n",
      "  Branch length: 0.746139\n",
      "\n",
      "Find internal nodes:\n",
      "\n",
      "      /-637389.Acaty_c1916\n",
      "   /-|\n",
      "--|   \\-637389.Acaty_c1239\n",
      "  |\n",
      "   \\-1158165.KB898877_gene1259\n",
      "\n",
      "Measure distances:\n",
      "branch lenght dist: 0.746139\n",
      "topology distance: 3.0\n",
      "\n",
      "Or even render an image of any node:\n"
     ]
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<IPython.core.display.Image object>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Lest's grab the first list in the list\n",
    "t = all_trees[\"555778.Hneap_1768\"]\n",
    "\n",
    "# Now let's explore basic operations: \n",
    "\n",
    "print(\"We can quickly print it:\")\n",
    "print(t)\n",
    "\n",
    "print(\"\\nGet the list of species and sequences included:\")\n",
    "print(\"  Species in tree:\", t.get_species())\n",
    "print(\"  Seqs in tree:\", t.get_leaf_names())\n",
    "\n",
    "\n",
    "print(\"\\nFind nodes by name and read attributes:\")\n",
    "leaf_node = t & \"1158165.KB898877_gene1259\"\n",
    "print(\"           Name:\", leaf_node.name)\n",
    "print(\"        Species:\", leaf_node.species)\n",
    "print(\"  Branch length:\", leaf_node.dist)\n",
    "\n",
    "\n",
    "print(\"\\nFind internal nodes:\")\n",
    "internal_node = t.get_common_ancestor(\"1158165.KB898877_gene1259\", \"637389.Acaty_c1916\")\n",
    "print(internal_node)\n",
    "\n",
    "print(\"\\nMeasure distances:\")\n",
    "distance = t.get_distance(internal_node, leaf_node)\n",
    "topo_distance = t.get_distance(\"525897.Dbac_2405\", leaf_node, topology_only=True)\n",
    "print(\"branch lenght dist:\", distance)\n",
    "print(\"topology distance:\", topo_distance)\n",
    "\n",
    "print(\"\\nOr even render an image of any node:\")\n",
    "internal_node.render('%%inline')\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### You can interact with the trees using a Graphical User Interface (GUI)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Load a tree and view \n",
    "t = all_trees[\"555778.Hneap_1768\"]\n",
    "t.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "(note that any modification done with the GUI, is kept in the tree instance when you close the GUI)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "   /-637389.Acaty_c1916\n",
      "--|\n",
      "  |   /-637389.Acaty_c1239\n",
      "   \\-|\n",
      "     |   /-1158165.KB898877_gene1259\n",
      "      \\-|\n",
      "        |   /-525897.Dbac_2405\n",
      "         \\-|\n",
      "            \\-555778.Hneap_1768\n"
     ]
    }
   ],
   "source": [
    "# print back after a mofication\n",
    "print(t)"
   ]
  }
 ],
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