prepare-big-file.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-08-10T23:46:24.623490Z",
     "start_time": "2023-08-10T23:46:18.058607Z"
    }
   },
   "outputs": [],
   "source": [
    "import os\n",
    "import pandas as pd\n",
    "from qiime2 import Artifact\n",
    "from qiime2 import Visualization\n",
    "from qiime2 import Metadata\n",
    "from qiime2.plugins import demux\n",
    "from qiime2.plugins.metadata.visualizers import tabulate\n",
    "import qiime2.plugins.dada2.actions as dada2_actions\n",
    "import qiime2.plugins.metadata.actions as metadata_actions\n",
    "from qiime2.plugins.feature_table.visualizers import tabulate_seqs\n",
    "from qiime2.plugins.feature_table.visualizers import summarize\n",
    "from qiime2.plugins.feature_table.visualizers import core_features\n",
    "#from qiime2.plugins.feature_table.methods import filter_samples\n",
    "from qiime2.plugins.demux.methods import filter_samples\n",
    "from qiime2.plugins.feature_table.methods import filter_seqs\n",
    "\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-08-10T23:46:24.628090Z",
     "start_time": "2023-08-10T23:46:24.625443Z"
    }
   },
   "outputs": [],
   "source": [
    "raw_data_path = os.path.join('.', 'data', 'raw')\n",
    "interim_data_path = os.path.join('.', 'data', 'interim')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-08-10T23:46:24.642283Z",
     "start_time": "2023-08-10T23:46:24.629454Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(40, 4)"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "metadata_path = os.path.join(raw_data_path, 'metadata-all-ana-types.tsv')\n",
    "metadata_qa = Metadata.load(metadata_path)\n",
    "metadata_df = pd.read_csv(metadata_path, sep='\\t', skiprows=[1])\n",
    "metadata_df.shape\n",
    "# metadata_df.head()\n",
    "#tabulate(metadata_qa).visualization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-08-10T23:49:33.036091Z",
     "start_time": "2023-08-10T23:46:24.644035Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div><img onload=\"(function(div, url){\n",
       "if (typeof require !== 'undefined') {\n",
       "    var baseURL = require.toUrl('').split('/').slice(0, -2).join('/');\n",
       "} else {\n",
       "    var baseURL = JSON.parse(\n",
       "        document.getElementById('jupyter-config-data').innerHTML\n",
       "    ).baseUrl.slice(0, -1);\n",
       "}\n",
       "url = baseURL + url;\n",
       "fetch(url).then(function(res) {\n",
       "    if (res.status === 404) {\n",
       "        div.innerHTML = 'Install QIIME 2 Jupyter extension with:<br />' +\n",
       "                        '<code>jupyter serverextension enable --py qiime2' +\n",
       "                        ' --sys-prefix</code><br />then restart your server.' +\n",
       "                        '<br /><br />(Interactive output not available on ' +\n",
       "                        'static notebook viewer services like nbviewer.)';\n",
       "    } else if (res.status === 409) {\n",
       "        div.innerHTML = 'Visualization no longer in scope. Re-run this cell' +\n",
       "                        ' to see the visualization.';\n",
       "    } else if (res.ok) {\n",
       "        url = res.url;\n",
       "        div.innerHTML = '<iframe src=\\'' + url + '\\' style=\\'' +\n",
       "                        'width: 100%; height: 700px; border: 0;\\'>' +\n",
       "                        '</iframe><hr />Open in a: <a href=\\'' + url + '\\'' +\n",
       "                        ' target=\\'_blank\\'>new window</a>'\n",
       "    } else {\n",
       "        div.innerHTML = 'Something has gone wrong. Check notebook server for' +\n",
       "                        ' errors.';\n",
       "    }\n",
       "});\n",
       "})(this.parentElement, '/qiime2/redirect?location=/tmp/qiime2-archive-m1jprkeo')\" src=\"data:image/gif;base64,R0lGODlhAQABAIAAAP///wAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw==\" /></div>"
      ],
      "text/plain": [
       "<visualization: Visualization uuid: 6e79ed9f-730c-41be-bb42-563a51139bf4>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "text/plain": [
       "<Figure size 432x288 with 0 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "demux_path = os.path.join(interim_data_path, 'demux-paired.qza')\n",
    "demux_qa = Artifact.load(demux_path)\n",
    "demux_view = demux.visualizers.summarize(demux_qa)\n",
    "demux_view.visualization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-08-10T23:49:36.365650Z",
     "start_time": "2023-08-10T23:49:33.038405Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<artifact: SampleData[PairedEndSequencesWithQuality] uuid: 4cd68957-18d3-4e10-9b26-3a0a896291c0>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from qiime2.plugins.demux.methods import filter_samples\n",
    "#from qiime2.plugins.feature_table.methods import filter_samples\n",
    "\n",
    "filtered_demux_qa = filter_samples(demux=demux_qa, metadata=metadata_qa).filtered_demux\n",
    "filtered_demux_qa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-08-10T23:54:31.749895Z",
     "start_time": "2023-08-10T23:52:51.881799Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div><img onload=\"(function(div, url){\n",
       "if (typeof require !== 'undefined') {\n",
       "    var baseURL = require.toUrl('').split('/').slice(0, -2).join('/');\n",
       "} else {\n",
       "    var baseURL = JSON.parse(\n",
       "        document.getElementById('jupyter-config-data').innerHTML\n",
       "    ).baseUrl.slice(0, -1);\n",
       "}\n",
       "url = baseURL + url;\n",
       "fetch(url).then(function(res) {\n",
       "    if (res.status === 404) {\n",
       "        div.innerHTML = 'Install QIIME 2 Jupyter extension with:<br />' +\n",
       "                        '<code>jupyter serverextension enable --py qiime2' +\n",
       "                        ' --sys-prefix</code><br />then restart your server.' +\n",
       "                        '<br /><br />(Interactive output not available on ' +\n",
       "                        'static notebook viewer services like nbviewer.)';\n",
       "    } else if (res.status === 409) {\n",
       "        div.innerHTML = 'Visualization no longer in scope. Re-run this cell' +\n",
       "                        ' to see the visualization.';\n",
       "    } else if (res.ok) {\n",
       "        url = res.url;\n",
       "        div.innerHTML = '<iframe src=\\'' + url + '\\' style=\\'' +\n",
       "                        'width: 100%; height: 700px; border: 0;\\'>' +\n",
       "                        '</iframe><hr />Open in a: <a href=\\'' + url + '\\'' +\n",
       "                        ' target=\\'_blank\\'>new window</a>'\n",
       "    } else {\n",
       "        div.innerHTML = 'Something has gone wrong. Check notebook server for' +\n",
       "                        ' errors.';\n",
       "    }\n",
       "});\n",
       "})(this.parentElement, '/qiime2/redirect?location=/tmp/qiime2-archive-0p4f15cm')\" src=\"data:image/gif;base64,R0lGODlhAQABAIAAAP///wAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw==\" /></div>"
      ],
      "text/plain": [
       "<visualization: Visualization uuid: 5cf123eb-e7c8-4a7f-b1a9-95907f747985>"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "text/plain": [
       "<Figure size 432x288 with 0 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "filtered_demux_view = demux.visualizers.summarize(filtered_demux_qa)\n",
    "filtered_demux_view.visualization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-08-10T23:49:36.379737Z",
     "start_time": "2023-08-10T23:49:36.367938Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\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>sample-id</th>\n",
       "      <th>sample-name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>210421121673</td>\n",
       "      <td>#1 N9.01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>210421121674</td>\n",
       "      <td>#2 N11.01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>210421121675</td>\n",
       "      <td>#3 N9.05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>210421121676</td>\n",
       "      <td>#4 N11.02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>210421121677</td>\n",
       "      <td>#5 N9.03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>210707163913</td>\n",
       "      <td>#70 7d.AM2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>210707163914</td>\n",
       "      <td>#71 7d.C3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>71</th>\n",
       "      <td>210707163915</td>\n",
       "      <td>#72 7d.M3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>72</th>\n",
       "      <td>210707163916</td>\n",
       "      <td>#73 7d.A3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>73</th>\n",
       "      <td>210707163917</td>\n",
       "      <td>#74 7d.AM3</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>74 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       sample-id sample-name\n",
       "0   210421121673    #1 N9.01\n",
       "1   210421121674   #2 N11.01\n",
       "2   210421121675    #3 N9.05\n",
       "3   210421121676   #4 N11.02\n",
       "4   210421121677    #5 N9.03\n",
       "..           ...         ...\n",
       "69  210707163913  #70 7d.AM2\n",
       "70  210707163914   #71 7d.C3\n",
       "71  210707163915   #72 7d.M3\n",
       "72  210707163916   #73 7d.A3\n",
       "73  210707163917  #74 7d.AM3\n",
       "\n",
       "[74 rows x 2 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Load relation FileID - SampleName\n",
    "relation_df = pd.read_csv(os.path.join(raw_data_path, 'sample_id-sample_name.tsv'), sep='\\t')\n",
    "relation_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-08-10T23:49:36.546802Z",
     "start_time": "2023-08-10T23:49:36.381528Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\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>sample-id</th>\n",
       "      <th>forward-path</th>\n",
       "      <th>reverse-path</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>210421121673</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>210421121674</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>210421121675</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>210421121676</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>210421121677</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>210707163913</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>210707163914</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>71</th>\n",
       "      <td>210707163915</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>72</th>\n",
       "      <td>210707163916</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>73</th>\n",
       "      <td>210707163917</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>74 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       sample-id                                       forward-path  \\\n",
       "0   210421121673  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "1   210421121674  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "2   210421121675  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "3   210421121676  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "4   210421121677  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "..           ...                                                ...   \n",
       "69  210707163913  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "70  210707163914  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "71  210707163915  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "72  210707163916  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "73  210707163917  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "\n",
       "                                         reverse-path  \n",
       "0   /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "1   /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "2   /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "3   /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "4   /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "..                                                ...  \n",
       "69  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "70  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "71  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "72  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "73  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "\n",
       "[74 rows x 3 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Load manifest list\n",
    "manifest_df = pd.read_csv(os.path.join(raw_data_path, 'karina-samples-groups.csv'))\n",
    "manifest_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-08-10T23:49:36.599320Z",
     "start_time": "2023-08-10T23:49:36.549262Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\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>sample-id</th>\n",
       "      <th>absolute-filepath</th>\n",
       "      <th>direction</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>210421121673</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>forward</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>210421121673</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>reverse</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>210421121674</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>forward</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>210421121674</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>reverse</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>210421121675</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>forward</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>143</th>\n",
       "      <td>210707163915</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>reverse</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>144</th>\n",
       "      <td>210707163916</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>forward</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>145</th>\n",
       "      <td>210707163916</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>reverse</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>146</th>\n",
       "      <td>210707163917</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>forward</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>147</th>\n",
       "      <td>210707163917</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>reverse</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>148 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        sample-id                                  absolute-filepath direction\n",
       "0    210421121673  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   forward\n",
       "1    210421121673  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   reverse\n",
       "2    210421121674  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   forward\n",
       "3    210421121674  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   reverse\n",
       "4    210421121675  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   forward\n",
       "..            ...                                                ...       ...\n",
       "143  210707163915  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   reverse\n",
       "144  210707163916  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   forward\n",
       "145  210707163916  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   reverse\n",
       "146  210707163917  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   forward\n",
       "147  210707163917  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   reverse\n",
       "\n",
       "[148 rows x 3 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "manifest2_df = pd.read_csv(os.path.join(raw_data_path, 'samples-paths.tsv'), sep='\\t')\n",
    "manifest2_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-08-10T23:49:36.616221Z",
     "start_time": "2023-08-10T23:49:36.601608Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\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>sample-id</th>\n",
       "      <th>forward-path</th>\n",
       "      <th>reverse-path</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>#1 N9.01</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>#2 N11.01</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>#3 N9.05</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>#4 N11.02</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>#5 N9.03</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>#70 7d.AM2</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>#71 7d.C3</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>71</th>\n",
       "      <td>#72 7d.M3</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>72</th>\n",
       "      <td>#73 7d.A3</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>73</th>\n",
       "      <td>#74 7d.AM3</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>74 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     sample-id                                       forward-path  \\\n",
       "0     #1 N9.01  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "1    #2 N11.01  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "2     #3 N9.05  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "3    #4 N11.02  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "4     #5 N9.03  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "..         ...                                                ...   \n",
       "69  #70 7d.AM2  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "70   #71 7d.C3  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "71   #72 7d.M3  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "72   #73 7d.A3  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "73  #74 7d.AM3  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   \n",
       "\n",
       "                                         reverse-path  \n",
       "0   /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "1   /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "2   /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "3   /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "4   /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "..                                                ...  \n",
       "69  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "70  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "71  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "72  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "73  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...  \n",
       "\n",
       "[74 rows x 3 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Join relation and manifest\n",
    "joined_df = pd.merge(relation_df, manifest_df, on='sample-id')\n",
    "joined_df = joined_df.drop(columns=['sample-id'])\n",
    "joined_df = joined_df.rename(columns={'sample-name': 'sample-id'})\n",
    "joined_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-08-10T23:49:36.651276Z",
     "start_time": "2023-08-10T23:49:36.619627Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\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>sample-id</th>\n",
       "      <th>absolute-filepath</th>\n",
       "      <th>direction</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>210421121673</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>forward</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>210421121673</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>reverse</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>210421121674</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>forward</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>210421121674</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>reverse</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>210421121675</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>forward</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>143</th>\n",
       "      <td>210707163915</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>reverse</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>144</th>\n",
       "      <td>210707163916</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>forward</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>145</th>\n",
       "      <td>210707163916</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>reverse</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>146</th>\n",
       "      <td>210707163917</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>forward</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>147</th>\n",
       "      <td>210707163917</td>\n",
       "      <td>/home/lauro/nupeb/dados_brutos_rede_genoma/dat...</td>\n",
       "      <td>reverse</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>148 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        sample-id                                  absolute-filepath direction\n",
       "0    210421121673  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   forward\n",
       "1    210421121673  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   reverse\n",
       "2    210421121674  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   forward\n",
       "3    210421121674  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   reverse\n",
       "4    210421121675  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   forward\n",
       "..            ...                                                ...       ...\n",
       "143  210707163915  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   reverse\n",
       "144  210707163916  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   forward\n",
       "145  210707163916  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   reverse\n",
       "146  210707163917  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   forward\n",
       "147  210707163917  /home/lauro/nupeb/dados_brutos_rede_genoma/dat...   reverse\n",
       "\n",
       "[148 rows x 3 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Join relation and manifest2\n",
    "joined2_df = pd.merge(relation_df, manifest2_df, on='sample-id')\n",
    "# joined2_df = joined2_df.drop(columns=['sample-id'])\n",
    "# joined2_df = joined2_df.rename(columns={'sample-name': 'sample-id'})\n",
    "# write to file\n",
    "manifest_cols = ['sample-id', 'absolute-filepath', 'direction']\n",
    "out_manifest = joined2_df[manifest_cols]\n",
    "out_manifest.to_csv(os.path.join(raw_data_path, 'manifest-all-ana.csv'), index=False)\n",
    "out_manifest"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-08-10T23:49:36.719319Z",
     "start_time": "2023-08-10T23:49:36.652856Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\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>sample-id</th>\n",
       "      <th>sample-name</th>\n",
       "      <th>sample-name-redux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>210421121673</td>\n",
       "      <td>#1 N9.01</td>\n",
       "      <td>N9.01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>210421121674</td>\n",
       "      <td>#2 N11.01</td>\n",
       "      <td>N11.01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>210421121675</td>\n",
       "      <td>#3 N9.05</td>\n",
       "      <td>N9.05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>210421121676</td>\n",
       "      <td>#4 N11.02</td>\n",
       "      <td>N11.02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>210421121677</td>\n",
       "      <td>#5 N9.03</td>\n",
       "      <td>N9.03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>210707163913</td>\n",
       "      <td>#70 7d.AM2</td>\n",
       "      <td>7d.AM2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>210707163914</td>\n",
       "      <td>#71 7d.C3</td>\n",
       "      <td>7d.C3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>71</th>\n",
       "      <td>210707163915</td>\n",
       "      <td>#72 7d.M3</td>\n",
       "      <td>7d.M3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>72</th>\n",
       "      <td>210707163916</td>\n",
       "      <td>#73 7d.A3</td>\n",
       "      <td>7d.A3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>73</th>\n",
       "      <td>210707163917</td>\n",
       "      <td>#74 7d.AM3</td>\n",
       "      <td>7d.AM3</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>74 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       sample-id sample-name sample-name-redux\n",
       "0   210421121673    #1 N9.01             N9.01\n",
       "1   210421121674   #2 N11.01            N11.01\n",
       "2   210421121675    #3 N9.05             N9.05\n",
       "3   210421121676   #4 N11.02            N11.02\n",
       "4   210421121677    #5 N9.03             N9.03\n",
       "..           ...         ...               ...\n",
       "69  210707163913  #70 7d.AM2            7d.AM2\n",
       "70  210707163914   #71 7d.C3             7d.C3\n",
       "71  210707163915   #72 7d.M3             7d.M3\n",
       "72  210707163916   #73 7d.A3             7d.A3\n",
       "73  210707163917  #74 7d.AM3            7d.AM3\n",
       "\n",
       "[74 rows x 3 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "relation_df['sample-name-redux'] = relation_df['sample-name'].str.split(' ').str[1]\n",
    "relation_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-08-10T23:49:36.736544Z",
     "start_time": "2023-08-10T23:49:36.721587Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\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>sample-name</th>\n",
       "      <th>group-id</th>\n",
       "      <th>group-desc</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>N9.01</td>\n",
       "      <td>NC</td>\n",
       "      <td>Ninhada controle</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>N11.01</td>\n",
       "      <td>NC</td>\n",
       "      <td>Ninhada controle</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>N9.05</td>\n",
       "      <td>NC</td>\n",
       "      <td>Ninhada controle</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>N11.02</td>\n",
       "      <td>NC</td>\n",
       "      <td>Ninhada controle</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>N9.03</td>\n",
       "      <td>NR</td>\n",
       "      <td>Ninhada reduzida</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>N10.03</td>\n",
       "      <td>NR</td>\n",
       "      <td>Ninhada reduzida</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>N10.04</td>\n",
       "      <td>NR</td>\n",
       "      <td>Ninhada reduzida</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>N10.07</td>\n",
       "      <td>NR</td>\n",
       "      <td>Ninhada reduzida</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>N10.08</td>\n",
       "      <td>NR</td>\n",
       "      <td>Ninhada reduzida</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>N7.01</td>\n",
       "      <td>STD-NC</td>\n",
       "      <td>Grupo dieta padrão</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>N7.02</td>\n",
       "      <td>STD-NC</td>\n",
       "      <td>Grupo dieta padrão</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>N8.01</td>\n",
       "      <td>STD-NC</td>\n",
       "      <td>Grupo dieta padrão</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>N1.01</td>\n",
       "      <td>STD-NC</td>\n",
       "      <td>Grupo dieta padrão</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>N3.01</td>\n",
       "      <td>STD-NC</td>\n",
       "      <td>Grupo dieta padrão</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>N4.01</td>\n",
       "      <td>STD-NC</td>\n",
       "      <td>Grupo dieta padrão</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>N4.02</td>\n",
       "      <td>STD-NC</td>\n",
       "      <td>Grupo dieta padrão</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>N7.03</td>\n",
       "      <td>STD-NR</td>\n",
       "      <td>Grupo dieta padrão</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>N7.04</td>\n",
       "      <td>STD-NR</td>\n",
       "      <td>Grupo dieta padrão</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>N8.03</td>\n",
       "      <td>STD-NR</td>\n",
       "      <td>Grupo dieta padrão</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>N1.02</td>\n",
       "      <td>STD-NR</td>\n",
       "      <td>Grupo dieta padrão</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>N1.03</td>\n",
       "      <td>STD-NR</td>\n",
       "      <td>Grupo dieta padrão</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>N2.02</td>\n",
       "      <td>STD-NR</td>\n",
       "      <td>Grupo dieta padrão</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>N2.03</td>\n",
       "      <td>STD-NR</td>\n",
       "      <td>Grupo dieta padrão</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>N7.05</td>\n",
       "      <td>HSD-NC</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>N8.05</td>\n",
       "      <td>HSD-NC</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>N8.06</td>\n",
       "      <td>HSD-NC</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>N1.04</td>\n",
       "      <td>HSD-NC</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>N2.04</td>\n",
       "      <td>HSD-NC</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>N3.04</td>\n",
       "      <td>HSD-NC</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>N4.03</td>\n",
       "      <td>HSD-NC</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>N4.04</td>\n",
       "      <td>HSD-NC</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>N7.07</td>\n",
       "      <td>HSD-NR</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>N7.08</td>\n",
       "      <td>HSD-NR</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>N8.08</td>\n",
       "      <td>HSD-NR</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>N1.05</td>\n",
       "      <td>HSD-NR</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>N2.05</td>\n",
       "      <td>HSD-NR</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>N3.05</td>\n",
       "      <td>HSD-NR</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>N3.06</td>\n",
       "      <td>HSD-NR</td>\n",
       "      <td>Grupo dieta high-sugar</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   sample-name group-id              group-desc\n",
       "0        N9.01       NC        Ninhada controle\n",
       "1       N11.01       NC        Ninhada controle\n",
       "2        N9.05       NC        Ninhada controle\n",
       "3       N11.02       NC        Ninhada controle\n",
       "4        N9.03       NR        Ninhada reduzida\n",
       "5       N10.03       NR        Ninhada reduzida\n",
       "6       N10.04       NR        Ninhada reduzida\n",
       "7       N10.07       NR        Ninhada reduzida\n",
       "8       N10.08       NR        Ninhada reduzida\n",
       "9        N7.01   STD-NC      Grupo dieta padrão\n",
       "10       N7.02   STD-NC      Grupo dieta padrão\n",
       "11       N8.01   STD-NC      Grupo dieta padrão\n",
       "12       N1.01   STD-NC      Grupo dieta padrão\n",
       "13       N3.01   STD-NC      Grupo dieta padrão\n",
       "14       N4.01   STD-NC      Grupo dieta padrão\n",
       "15       N4.02   STD-NC      Grupo dieta padrão\n",
       "16       N7.03   STD-NR      Grupo dieta padrão\n",
       "17       N7.04   STD-NR      Grupo dieta padrão\n",
       "18       N8.03   STD-NR      Grupo dieta padrão\n",
       "19       N1.02   STD-NR      Grupo dieta padrão\n",
       "20       N1.03   STD-NR      Grupo dieta padrão\n",
       "21       N2.02   STD-NR      Grupo dieta padrão\n",
       "22       N2.03   STD-NR      Grupo dieta padrão\n",
       "23       N7.05   HSD-NC  Grupo dieta high-sugar\n",
       "24       N8.05   HSD-NC  Grupo dieta high-sugar\n",
       "25       N8.06   HSD-NC  Grupo dieta high-sugar\n",
       "26       N1.04   HSD-NC  Grupo dieta high-sugar\n",
       "27       N2.04   HSD-NC  Grupo dieta high-sugar\n",
       "28       N3.04   HSD-NC  Grupo dieta high-sugar\n",
       "29       N4.03   HSD-NC  Grupo dieta high-sugar\n",
       "30       N4.04   HSD-NC  Grupo dieta high-sugar\n",
       "31       N7.07   HSD-NR  Grupo dieta high-sugar\n",
       "32       N7.08   HSD-NR  Grupo dieta high-sugar\n",
       "33       N8.08   HSD-NR  Grupo dieta high-sugar\n",
       "34       N1.05   HSD-NR  Grupo dieta high-sugar\n",
       "35       N2.05   HSD-NR  Grupo dieta high-sugar\n",
       "36       N3.05   HSD-NR  Grupo dieta high-sugar\n",
       "37       N3.06   HSD-NR  Grupo dieta high-sugar"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "metadata_df = pd.read_csv(os.path.join(raw_data_path, 'ana-flavia-samples-groups.tsv'), sep='\\t')\n",
    "metadata_df = metadata_df.rename(columns={'sample-id': 'sample-name'})\n",
    "metadata_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-08-10T23:49:36.746887Z",
     "start_time": "2023-08-10T23:49:36.738695Z"
    }
   },
   "outputs": [],
   "source": [
    "joined_metadata_df = pd.merge(relation_df, metadata_df, left_on='sample-name-redux', right_on='sample-name')\n",
    "joined_metadata_df = joined_metadata_df[['sample-id', 'sample-name-redux', 'group-id', 'group-desc']].rename(columns={'sample-name-redux': 'sample-name'})\n",
    "joined_metadata_df.to_csv(os.path.join(raw_data_path, 'metadata-all-ana.tsv'), sep='\\t', index=False)"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "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": "3.8.12"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 1
}