{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "res = pd.read_csv(\"species_cranky_wozniak\", sep = \"\\t\", header = None, \n",
    "                  names = ['taxid', 'rank', 'taxpath', 'taxpathsn', 'percentage'],\n",
    "                 skiprows= 1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxid</th>\n",
       "      <th>rank</th>\n",
       "      <th>taxpath</th>\n",
       "      <th>taxpathsn</th>\n",
       "      <th>percentage</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>56636</td>\n",
       "      <td>species</td>\n",
       "      <td>2157|28889|183924|114380|2272|56635|56636</td>\n",
       "      <td>Archaea|Crenarchaeota|Thermoprotei|Desulfuroco...</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>477693</td>\n",
       "      <td>species</td>\n",
       "      <td>2157|28889|183924|114380|2272|2273|477693</td>\n",
       "      <td>Archaea|Crenarchaeota|Thermoprotei|Desulfuroco...</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>160233</td>\n",
       "      <td>species</td>\n",
       "      <td>2157|28889|183924|114380|2272|54258|160233</td>\n",
       "      <td>Archaea|Crenarchaeota|Thermoprotei|Desulfuroco...</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>54248</td>\n",
       "      <td>species</td>\n",
       "      <td>2157|28889|183924|114380|2307|54247|54248</td>\n",
       "      <td>Archaea|Crenarchaeota|Thermoprotei|Desulfuroco...</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>2285</td>\n",
       "      <td>species</td>\n",
       "      <td>2157|28889|183924|2281|118883|2284|2285</td>\n",
       "      <td>Archaea|Crenarchaeota|Thermoprotei|Sulfolobale...</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    taxid     rank                                     taxpath  \\\n",
       "0   56636  species   2157|28889|183924|114380|2272|56635|56636   \n",
       "1  477693  species   2157|28889|183924|114380|2272|2273|477693   \n",
       "2  160233  species  2157|28889|183924|114380|2272|54258|160233   \n",
       "3   54248  species   2157|28889|183924|114380|2307|54247|54248   \n",
       "4    2285  species     2157|28889|183924|2281|118883|2284|2285   \n",
       "\n",
       "                                           taxpathsn  percentage  \n",
       "0  Archaea|Crenarchaeota|Thermoprotei|Desulfuroco...         0.0  \n",
       "1  Archaea|Crenarchaeota|Thermoprotei|Desulfuroco...         0.0  \n",
       "2  Archaea|Crenarchaeota|Thermoprotei|Desulfuroco...         0.0  \n",
       "3  Archaea|Crenarchaeota|Thermoprotei|Desulfuroco...         0.0  \n",
       "4  Archaea|Crenarchaeota|Thermoprotei|Sulfolobale...         0.0  "
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "res.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(1029, 5)"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "res.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "def summarize_all_levels(df, ranks):\n",
    "    new_rows = []\n",
    "\n",
    "    for (_, _, taxpath, taxpathsn, percentage) in df.itertuples(index=False, name=None):\n",
    "        lineage_values = taxpath.split(\"|\")\n",
    "        lineage_names = taxpathsn.split(\"|\")\n",
    "\n",
    "        for i, (rank, tax_id) in enumerate(zip(ranks[:-1], lineage_values), 1):\n",
    "            taxpath = \"|\".join(lineage_values[:i])\n",
    "            taxpathsn = \"|\".join(lineage_names[:i])\n",
    "            new_rows.append([tax_id, rank, taxpath, taxpathsn, percentage])\n",
    "\n",
    "    new_df = pd.DataFrame(new_rows, columns=df.columns)\n",
    "    return new_df.groupby(\n",
    "        ['taxid', 'rank', 'taxpath', 'taxpathsn'], as_index=False\n",
    "    ).sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "tax_ranks = ranks = \"superkingdom|phylum|class|order|family|genus|species\".split(\"|\")\n",
    "new_df = summarize_all_levels(res, tax_ranks)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxid</th>\n",
       "      <th>rank</th>\n",
       "      <th>taxpath</th>\n",
       "      <th>taxpathsn</th>\n",
       "      <th>percentage</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>10</td>\n",
       "      <td>genus</td>\n",
       "      <td>2|1224|1236|72274|135621|10</td>\n",
       "      <td>Bacteria|Proteobacteria|Gammaproteobacteria|Ps...</td>\n",
       "      <td>0.010060</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>100715</td>\n",
       "      <td>genus</td>\n",
       "      <td>2|1090|191410|191411|191412|100715</td>\n",
       "      <td>Bacteria|Chlorobi|Chlorobia|Chlorobiales|Chlor...</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>100883</td>\n",
       "      <td>genus</td>\n",
       "      <td>2|1239|526524|526525|128827|100883</td>\n",
       "      <td>Bacteria|Firmicutes|Erysipelotrichia|Erysipelo...</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1016</td>\n",
       "      <td>genus</td>\n",
       "      <td>2|976|117743|200644|49546|1016</td>\n",
       "      <td>Bacteria|Bacteroidetes|Flavobacteriia|Flavobac...</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1021</td>\n",
       "      <td>genus</td>\n",
       "      <td>2|1224|1236|72273|135617|1021</td>\n",
       "      <td>Bacteria|Proteobacteria|Gammaproteobacteria|Th...</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1033</th>\n",
       "      <td>97050</td>\n",
       "      <td>genus</td>\n",
       "      <td>2|1224|28211|204455|31989|97050</td>\n",
       "      <td>Bacteria|Proteobacteria|Alphaproteobacteria|Rh...</td>\n",
       "      <td>0.191146</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1034</th>\n",
       "      <td>972</td>\n",
       "      <td>family</td>\n",
       "      <td>2|1239|186801|53433|972</td>\n",
       "      <td>Bacteria|Firmicutes|Clostridia|Halanaerobiales...</td>\n",
       "      <td>0.010060</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1035</th>\n",
       "      <td>976</td>\n",
       "      <td>phylum</td>\n",
       "      <td>2|976</td>\n",
       "      <td>Bacteria|Bacteroidetes</td>\n",
       "      <td>2.263578</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1036</th>\n",
       "      <td>978</td>\n",
       "      <td>genus</td>\n",
       "      <td>2|976|768503|768507|89373|978</td>\n",
       "      <td>Bacteria|Bacteroidetes|Cytophagia|Cytophagales...</td>\n",
       "      <td>0.010060</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1037</th>\n",
       "      <td>995019</td>\n",
       "      <td>family</td>\n",
       "      <td>2|1224|28216|80840|995019</td>\n",
       "      <td>Bacteria|Proteobacteria|Betaproteobacteria|Bur...</td>\n",
       "      <td>0.010060</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1038 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       taxid    rank                             taxpath  \\\n",
       "0         10   genus         2|1224|1236|72274|135621|10   \n",
       "1     100715   genus  2|1090|191410|191411|191412|100715   \n",
       "2     100883   genus  2|1239|526524|526525|128827|100883   \n",
       "3       1016   genus      2|976|117743|200644|49546|1016   \n",
       "4       1021   genus       2|1224|1236|72273|135617|1021   \n",
       "...      ...     ...                                 ...   \n",
       "1033   97050   genus     2|1224|28211|204455|31989|97050   \n",
       "1034     972  family             2|1239|186801|53433|972   \n",
       "1035     976  phylum                               2|976   \n",
       "1036     978   genus       2|976|768503|768507|89373|978   \n",
       "1037  995019  family           2|1224|28216|80840|995019   \n",
       "\n",
       "                                              taxpathsn  percentage  \n",
       "0     Bacteria|Proteobacteria|Gammaproteobacteria|Ps...    0.010060  \n",
       "1     Bacteria|Chlorobi|Chlorobia|Chlorobiales|Chlor...    0.000000  \n",
       "2     Bacteria|Firmicutes|Erysipelotrichia|Erysipelo...    0.000000  \n",
       "3     Bacteria|Bacteroidetes|Flavobacteriia|Flavobac...    0.000000  \n",
       "4     Bacteria|Proteobacteria|Gammaproteobacteria|Th...    0.000000  \n",
       "...                                                 ...         ...  \n",
       "1033  Bacteria|Proteobacteria|Alphaproteobacteria|Rh...    0.191146  \n",
       "1034  Bacteria|Firmicutes|Clostridia|Halanaerobiales...    0.010060  \n",
       "1035                             Bacteria|Bacteroidetes    2.263578  \n",
       "1036  Bacteria|Bacteroidetes|Cytophagia|Cytophagales...    0.010060  \n",
       "1037  Bacteria|Proteobacteria|Betaproteobacteria|Bur...    0.010060  \n",
       "\n",
       "[1038 rows x 5 columns]"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "new_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "94.30576299999994"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sum(res['percentage'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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