doc/using-LCA-database-API.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Using the `LCA_Database` API"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`LCA_Database` objects combine a fast in-memory storage of signatures\n",
    "indexed by their hash values, with taxonomic lineage storage.  They are\n",
    "limited to storing scaled DNA signatures with a single ksize; the scaled\n",
    "and ksize values are specified at creation."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Running this notebook.\n",
    "\n",
    "You can run this notebook interactively via mybinder; click on this button:\n",
    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dib-lab/sourmash/latest?labpath=doc%2Fusing-LCA-database-API.ipynb)\n",
    "\n",
    "A rendered version of this notebook is available at [sourmash.readthedocs.io](https://sourmash.readthedocs.io) under \"Tutorials and notebooks\".\n",
    "\n",
    "You can also get this notebook from the [doc/ subdirectory of the sourmash github repository](https://github.com/dib-lab/sourmash/tree/latest/doc). See [binder/environment.yaml](https://github.com/dib-lab/sourmash/blob/latest/binder/environment.yml) for installation dependencies.\n",
    "\n",
    "### What is this?\n",
    "\n",
    "This is a Jupyter Notebook using Python 3. If you are running this via [binder](https://mybinder.org), you can use Shift-ENTER to run cells, and double click on code cells to edit them.\n",
    "\n",
    "Contact: C. Titus Brown, ctbrown@ucdavis.edu. Please [file issues on GitHub](https://github.com/dib-lab/sourmash/issues/) if you have any questions or comments!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Creating an `LCA_Database` object\n",
    "\n",
    "Create an `LCA_Database` like so:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sourmash\n",
    "db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Create signatures for some genomes, load them, and add them:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\r",
      "\u001b[K\r\n",
      "== This is sourmash version 4.8.2. ==\r\n",
      "\r",
      "\u001b[K== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==\r\n",
      "\r\n",
      "\r",
      "\u001b[Kcomputing signatures for files: genomes/akkermansia.fa, genomes/shew_os185.fa, genomes/shew_os223.fa\r\n",
      "\r",
      "\u001b[KComputing a total of 1 signature(s) for each input.\r\n",
      "\r",
      "\u001b[Kskipping genomes/akkermansia.fa - already done\r\n",
      "\r",
      "\u001b[Kskipping genomes/shew_os185.fa - already done\r\n",
      "\r",
      "\u001b[Kskipping genomes/shew_os223.fa - already done\r\n"
     ]
    }
   ],
   "source": [
    "!sourmash sketch dna -p k=31,scaled=1000 genomes/*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "sig1 = sourmash.load_one_signature('akkermansia.fa.sig', ksize=31)\n",
    "sig2 = sourmash.load_one_signature('shew_os185.fa.sig', ksize=31)\n",
    "sig3 = sourmash.load_one_signature('shew_os223.fa.sig', ksize=31)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "490"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "db.insert(sig1, ident='akkermansia')\n",
    "db.insert(sig2, ident='shew_os185')\n",
    "db.insert(sig3, ident='shew_os223')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Run `search` and `gather` via the `Index` API"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[Result(score=1.0, signature=SourmashSignature('CP001071.1 Akkermansia muciniphila ATCC BAA-835, complete genome', 6822e0b7), location=None)]\n"
     ]
    }
   ],
   "source": [
    "from pprint import pprint\n",
    "pprint(db.search(sig1, threshold=0.1))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[Result(score=1.0, signature=SourmashSignature('NC_009665.1 Shewanella baltica OS185, complete genome', b47b13ef), location=None),\n",
      " Result(score=0.22846441947565543, signature=SourmashSignature('NC_011663.1 Shewanella baltica OS223, complete genome', ae6659f6), location=None)]\n"
     ]
    }
   ],
   "source": [
    "pprint(db.search(sig2, threshold=0.1))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Result(score=1.0, signature=SourmashSignature('NC_011663.1 Shewanella baltica OS223, complete genome', ae6659f6), location=None)\n"
     ]
    }
   ],
   "source": [
    "pprint(db.best_containment(sig3))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Retrieve all signatures with `signatures()`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CP001071.1 Akkermansia muciniphila ATCC BAA-835, complete genome\n",
      "NC_009665.1 Shewanella baltica OS185, complete genome\n",
      "NC_011663.1 Shewanella baltica OS223, complete genome\n"
     ]
    }
   ],
   "source": [
    "for i in db.signatures():\n",
    "    print(i)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Access identifiers and names"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The list of (unique) identifiers in the database can be accessed via the attribute `ident_to_idx`, which maps to integer identifiers; identifiers can also retrieve full names, which are taken from `sig.name()` upon insertion."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "dict_keys(['akkermansia', 'shew_os185', 'shew_os223'])\n"
     ]
    }
   ],
   "source": [
    "pprint(db._ident_to_idx.keys())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'akkermansia': 'CP001071.1 Akkermansia muciniphila ATCC BAA-835, complete '\n",
      "                'genome',\n",
      " 'shew_os185': 'NC_009665.1 Shewanella baltica OS185, complete genome',\n",
      " 'shew_os223': 'NC_011663.1 Shewanella baltica OS223, complete genome'}\n"
     ]
    }
   ],
   "source": [
    "pprint(db._ident_to_name)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Access hash values directly"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The attribute `_hashval_to_idx` contains a mapping from individual hash values to sets of `idx` indices.\n",
    "\n",
    "See the method `_find_signatures()` for an example of how this is used in `search` and `gather`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1300 hash values total in this database\n"
     ]
    }
   ],
   "source": [
    "print('{} hash values total in this database'.format(len(db._hashval_to_idx)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "belonging to signatures with idx {0, 1, 2}\n"
     ]
    }
   ],
   "source": [
    "all_idx = set()\n",
    "for idx_set in db._hashval_to_idx.values():\n",
    "    all_idx.update(idx_set)\n",
    "print('belonging to signatures with idx {}'.format(all_idx))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "first_three_hashvals = list(db._hashval_to_idx)[:3]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "hashval 17302105753387 belongs to idxs {0}\n",
      "hashval 95741036335406 belongs to idxs {0}\n",
      "hashval 165640715598232 belongs to idxs {0}\n"
     ]
    }
   ],
   "source": [
    "for hashval in first_three_hashvals:\n",
    "    print('hashval {} belongs to idxs {}'.format(hashval, db._hashval_to_idx[hashval]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "490 hashvals belong to query idx 2\n",
      "query idx 2 matches to ident shew_os223\n",
      "query idx 2 matches to name NC_011663.1 Shewanella baltica OS223, complete genome\n"
     ]
    }
   ],
   "source": [
    "query_idx = 2\n",
    "hashval_set = set()\n",
    "for hashval, idx_set in db._hashval_to_idx.items():\n",
    "    if query_idx in idx_set:\n",
    "        hashval_set.add(hashval)\n",
    "        \n",
    "print('{} hashvals belong to query idx {}'.format(len(hashval_set), query_idx))\n",
    "\n",
    "ident = db._idx_to_ident[query_idx]\n",
    "print('query idx {} matches to ident {}'.format(query_idx, ident))\n",
    "\n",
    "name = db._ident_to_name[ident]\n",
    "print('query idx {} matches to name {}'.format(query_idx, name))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Lineage storage and retrieval"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "from sourmash.lca.lca_utils import LineagePair"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "superkingdom = LineagePair('superkingdom', 'Bacteria')\n",
    "phylum = LineagePair('phylum', 'Verrucomicrobia')\n",
    "klass = LineagePair('class', 'Verrucomicrobiae')\n",
    "\n",
    "lineage = (superkingdom, phylum, klass)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "499"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)\n",
    "db.insert(sig1, lineage=lineage)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ident 'CP001071.1 Akkermansia muciniphila ATCC BAA-835, complete genome' has idx 0\n",
      "lid for idx 0 is 0\n",
      "lineage for lid 0 is Bacteria;Verrucomicrobia;Verrucomicrobiae\n"
     ]
    }
   ],
   "source": [
    "# by default, the identifier is the signature name --\n",
    "ident = sig1.name\n",
    "idx = db._ident_to_idx[ident]\n",
    "print(\"ident '{}' has idx {}\".format(ident, idx))\n",
    "\n",
    "lid = db._idx_to_lid[idx]\n",
    "print(\"lid for idx {} is {}\".format(idx, lid))\n",
    "\n",
    "lineage = db._lid_to_lineage[lid]\n",
    "display = sourmash.lca.display_lineage(lineage)\n",
    "print(\"lineage for lid {} is {}\".format(lid, display))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Lineage manipulation"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Default taxonomy ranks for lineages\n",
    "\n",
    "While sourmash lineage functions can work with any taxonomy ranks and any taxonomy names, both the NCBI and GTDB taxonomies use superkingdom/phylum/etc, so there is a hard coded list availalbe via `sourmash.lca.taxlist()`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['superkingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species', 'strain']\n"
     ]
    }
   ],
   "source": [
    "print(list(sourmash.lca.taxlist()))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Given a taxonomy as a list, you can then construct a lineage like so:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[LineagePair(rank='superkingdom', name='Bacteria'),\n",
      " LineagePair(rank='phylum', name='Verrucomicrobia'),\n",
      " LineagePair(rank='class', name='Verrucomicrobiae'),\n",
      " LineagePair(rank='order', name='Verrucomicrobiales'),\n",
      " LineagePair(rank='family', name='Akkermansiaceae'),\n",
      " LineagePair(rank='genus', name='Akkermansia'),\n",
      " LineagePair(rank='species', name='Akkermansia muciniphila'),\n",
      " LineagePair(rank='strain', name='Akkermansia muciniphila ATCC BAA-835')]\n"
     ]
    }
   ],
   "source": [
    "linstr1 = [\"Bacteria\", \"Verrucomicrobia\", \"Verrucomicrobiae\",\n",
    "           \"Verrucomicrobiales\", \"Akkermansiaceae\", \"Akkermansia\",\n",
    "           \"Akkermansia muciniphila\", \"Akkermansia muciniphila ATCC BAA-835\"]\n",
    "\n",
    "lineage1 = [ LineagePair(*pair) for pair in zip(sourmash.lca.taxlist(), linstr1) ]\n",
    "pprint(lineage1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835'"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# display lineages as strings with 'sourmash.lca.display_lineage()'\n",
    "sourmash.lca.display_lineage(lineage1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## sourmash lowest-common-ancestor functions"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The LCA functionality available in sourmash is built around some simple lineage manipulation functions -- `build_tree` and `find_lca`.\n",
    "\n",
    "First, let's define some more lineages --"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "lineage2 is Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Shewanellaceae;Shewanella;Shewanella baltica;Shewanella baltica OS185\n",
      "lineage3 is Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Shewanellaceae;Shewanella;Shewanella baltica;Shewanella baltica OS223\n"
     ]
    }
   ],
   "source": [
    "linstr2 = [\"Bacteria\", \"Proteobacteria\", \"Gammaproteobacteria\",\n",
    "           \"Alteromonadales\", \"Shewanellaceae\", \"Shewanella\",\n",
    "           \"Shewanella baltica\", \"Shewanella baltica OS185\"]\n",
    "lineage2 = [ LineagePair(*pair) for pair in zip(sourmash.lca.taxlist(), linstr2) ]\n",
    "\n",
    "linstr3 = [\"Bacteria\", \"Proteobacteria\", \"Gammaproteobacteria\",\n",
    "           \"Alteromonadales\", \"Shewanellaceae\", \"Shewanella\",\n",
    "           \"Shewanella baltica\", \"Shewanella baltica OS223\"]\n",
    "lineage3 = [ LineagePair(*pair) for pair in zip(sourmash.lca.taxlist(), linstr3) ]\n",
    "\n",
    "print('lineage2 is', sourmash.lca.display_lineage(lineage2))\n",
    "print('lineage3 is', sourmash.lca.display_lineage(lineage3))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now, build a tree structure that collapses these lineages where it can, and run some LCA analyses. Lineages 1 and 2 collapse to superkingdom:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "((LineagePair(rank='superkingdom', name='Bacteria'),), 2)"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tree = sourmash.lca.build_tree([lineage1, lineage2])\n",
    "sourmash.lca.find_lca(tree)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "while lineages 2 and 3 collapse to species:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "((LineagePair(rank='superkingdom', name='Bacteria'),\n",
       "  LineagePair(rank='phylum', name='Proteobacteria'),\n",
       "  LineagePair(rank='class', name='Gammaproteobacteria'),\n",
       "  LineagePair(rank='order', name='Alteromonadales'),\n",
       "  LineagePair(rank='family', name='Shewanellaceae'),\n",
       "  LineagePair(rank='genus', name='Shewanella'),\n",
       "  LineagePair(rank='species', name='Shewanella baltica')),\n",
       " 2)"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tree = sourmash.lca.build_tree([lineage2, lineage3])\n",
    "sourmash.lca.find_lca(tree)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Convenience functions let you make use of LCA_Database stored lineages"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "First, let's create a database from 3 signatures, and this time we'll store lineages in there:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "490"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)\n",
    "db.insert(sig1, lineage=lineage1)\n",
    "db.insert(sig2, lineage=lineage2)\n",
    "db.insert(sig3, lineage=lineage3)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now, for any collection of hashes, you can retrieve all the lineage assignments into a dictionary:\n",
    "`{ hashval: set of lineages }`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "num hashvals: 494\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/var/folders/6s/_f373w1d6hdfjc2kjstq97s80000gp/T/ipykernel_3384/490137846.py:1: DeprecatedWarning: get_mins is deprecated as of 3.5 and will be removed in 5.0. Use .hashes property instead.\n",
      "  assignments = sourmash.lca.gather_assignments(sig2.minhash.get_mins(), [db])\n"
     ]
    }
   ],
   "source": [
    "assignments = sourmash.lca.gather_assignments(sig2.minhash.get_mins(), [db])\n",
    "print('num hashvals:', len(assignments))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For example, this particular hashvalue belongs to two different lineages:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{(LineagePair(rank='superkingdom', name='Bacteria'),\n",
       "  LineagePair(rank='phylum', name='Proteobacteria'),\n",
       "  LineagePair(rank='class', name='Gammaproteobacteria'),\n",
       "  LineagePair(rank='order', name='Alteromonadales'),\n",
       "  LineagePair(rank='family', name='Shewanellaceae'),\n",
       "  LineagePair(rank='genus', name='Shewanella'),\n",
       "  LineagePair(rank='species', name='Shewanella baltica'),\n",
       "  LineagePair(rank='strain', name='Shewanella baltica OS185')),\n",
       " (LineagePair(rank='superkingdom', name='Bacteria'),\n",
       "  LineagePair(rank='phylum', name='Proteobacteria'),\n",
       "  LineagePair(rank='class', name='Gammaproteobacteria'),\n",
       "  LineagePair(rank='order', name='Alteromonadales'),\n",
       "  LineagePair(rank='family', name='Shewanellaceae'),\n",
       "  LineagePair(rank='genus', name='Shewanella'),\n",
       "  LineagePair(rank='species', name='Shewanella baltica'),\n",
       "  LineagePair(rank='strain', name='Shewanella baltica OS223'))}"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "assignments[196037984804395]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "sourmash also includes functions to summarize assignments by counting the number of\n",
    "times a particular lineage occurs; this is\n",
    "used by `sourmash lca classify` and `sourmash lca summarize`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "311 hashes have LCA: Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Shewanellaceae;Shewanella;Shewanella baltica;Shewanella baltica OS185\n",
      "183 hashes have LCA: Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Shewanellaceae;Shewanella;Shewanella baltica\n"
     ]
    }
   ],
   "source": [
    "counter = sourmash.lca.count_lca_for_assignments(assignments)\n",
    "\n",
    "# count_lca_for_assignments returns a collections.Counter object\n",
    "for lineage, count in counter.most_common():\n",
    "    print('{} hashes have LCA: {}'.format(count, sourmash.lca.display_lineage(lineage)))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Other pointers\n",
    "\n",
    "[Sourmash: a practical guide](https://sourmash.readthedocs.io/en/latest/using-sourmash-a-guide.html)\n",
    "\n",
    "[Classifying signatures taxonomically](https://sourmash.readthedocs.io/en/latest/classifying-signatures.html)\n",
    "\n",
    "[Pre-built search databases](https://sourmash.readthedocs.io/en/latest/databases.html)\n",
    "\n",
    "## A full list of notebooks\n",
    "\n",
    "[An introduction to k-mers for genome comparison and analysis](kmers-and-minhash.ipynb)\n",
    "\n",
    "[Some sourmash command line examples!](sourmash-examples.ipynb)\n",
    "\n",
    "[Working with private collections of signatures.](sourmash-collections.ipynb)\n",
    "\n",
    "[Using the LCA_Database API.](using-LCA-database-API.ipynb)"
   ]
  }
 ],
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