FPKM_Dividing_Timeseries_Study.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Goal: Dividing the lung FPKM according to ecah phenotype to a seperate csv file for model reconstruction "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "## Data Source: https://filetransfer.mdc-berlin.de/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "df1 = pd.read_csv('data/time_series_study/SupplementaryData2_Calu3_polyA_series1_fpkm.tsv',sep='\\t')\n",
    "df2 = pd.read_csv('data/time_series_study/SupplementaryData3_Calu3_polyA_series2_fpkm.tsv',sep='\\t')\n",
    "df3 = pd.read_csv('data/time_series_study/SupplementaryData5_H1299_polyA_fpkm.tsv',sep='\\t')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "dfs = [df1, df2, df3]\n",
    "dfs = [df.set_index('gene_id||gene_name').drop(columns=['length']) for df in dfs]\n",
    "df = dfs[0].join(dfs[1:])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "df['genes'] = df.index\n",
    "df.index = df['genes'].apply(lambda x:x.split('||')[1])\n",
    "df = df.drop(columns=['genes'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(45057, 60)"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Calu3_polyA_series1-S1-4h-A</th>\n",
       "      <th>Calu3_polyA_series1-S1-4h-B</th>\n",
       "      <th>Calu3_polyA_series1-S1-12h-A</th>\n",
       "      <th>Calu3_polyA_series1-S1-12h-B</th>\n",
       "      <th>Calu3_polyA_series1-S1-24h-A</th>\n",
       "      <th>Calu3_polyA_series1-S1-24h-A-detachedcells</th>\n",
       "      <th>Calu3_polyA_series1-S1-24h-B</th>\n",
       "      <th>Calu3_polyA_series1-S1-24h-B-detachedcells</th>\n",
       "      <th>Calu3_polyA_series1-S2-4h-A</th>\n",
       "      <th>Calu3_polyA_series1-S2-4h-B</th>\n",
       "      <th>...</th>\n",
       "      <th>H1299_polyA_S2-24h-A</th>\n",
       "      <th>H1299_polyA_S2-24h-B</th>\n",
       "      <th>H1299_polyA_S2-36h-A</th>\n",
       "      <th>H1299_polyA_S2-36h-B</th>\n",
       "      <th>H1299_polyA_mock-4h-A</th>\n",
       "      <th>H1299_polyA_mock-4h-B</th>\n",
       "      <th>H1299_polyA_mock-36h-A</th>\n",
       "      <th>H1299_polyA_mock-36h-B</th>\n",
       "      <th>H1299_polyA_untr-4h-A</th>\n",
       "      <th>H1299_polyA_untr-4h-B</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>genes</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ETV5-AS1</th>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LINC01299</th>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.154</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.029</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MLLT3</th>\n",
       "      <td>5.190</td>\n",
       "      <td>5.600</td>\n",
       "      <td>6.417</td>\n",
       "      <td>6.497</td>\n",
       "      <td>7.833</td>\n",
       "      <td>7.608</td>\n",
       "      <td>6.875</td>\n",
       "      <td>9.475</td>\n",
       "      <td>4.435</td>\n",
       "      <td>4.974</td>\n",
       "      <td>...</td>\n",
       "      <td>4.287</td>\n",
       "      <td>4.033</td>\n",
       "      <td>3.814</td>\n",
       "      <td>3.549</td>\n",
       "      <td>3.750</td>\n",
       "      <td>3.820</td>\n",
       "      <td>3.970</td>\n",
       "      <td>4.311</td>\n",
       "      <td>4.081</td>\n",
       "      <td>3.734</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SCGB3A2</th>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SEPT10P1</th>\n",
       "      <td>0.856</td>\n",
       "      <td>1.022</td>\n",
       "      <td>1.110</td>\n",
       "      <td>0.419</td>\n",
       "      <td>1.400</td>\n",
       "      <td>1.047</td>\n",
       "      <td>1.172</td>\n",
       "      <td>1.977</td>\n",
       "      <td>1.259</td>\n",
       "      <td>0.733</td>\n",
       "      <td>...</td>\n",
       "      <td>2.090</td>\n",
       "      <td>1.429</td>\n",
       "      <td>1.462</td>\n",
       "      <td>1.729</td>\n",
       "      <td>1.867</td>\n",
       "      <td>1.586</td>\n",
       "      <td>2.387</td>\n",
       "      <td>2.268</td>\n",
       "      <td>2.350</td>\n",
       "      <td>1.254</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 60 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "           Calu3_polyA_series1-S1-4h-A  Calu3_polyA_series1-S1-4h-B  \\\n",
       "genes                                                                 \n",
       "ETV5-AS1                         0.000                        0.000   \n",
       "LINC01299                        0.000                        0.000   \n",
       "MLLT3                            5.190                        5.600   \n",
       "SCGB3A2                          0.000                        0.000   \n",
       "SEPT10P1                         0.856                        1.022   \n",
       "\n",
       "           Calu3_polyA_series1-S1-12h-A  Calu3_polyA_series1-S1-12h-B  \\\n",
       "genes                                                                   \n",
       "ETV5-AS1                          0.000                         0.000   \n",
       "LINC01299                         0.000                         0.000   \n",
       "MLLT3                             6.417                         6.497   \n",
       "SCGB3A2                           0.000                         0.000   \n",
       "SEPT10P1                          1.110                         0.419   \n",
       "\n",
       "           Calu3_polyA_series1-S1-24h-A  \\\n",
       "genes                                     \n",
       "ETV5-AS1                          0.000   \n",
       "LINC01299                         0.000   \n",
       "MLLT3                             7.833   \n",
       "SCGB3A2                           0.000   \n",
       "SEPT10P1                          1.400   \n",
       "\n",
       "           Calu3_polyA_series1-S1-24h-A-detachedcells  \\\n",
       "genes                                                   \n",
       "ETV5-AS1                                        0.000   \n",
       "LINC01299                                       0.154   \n",
       "MLLT3                                           7.608   \n",
       "SCGB3A2                                         0.000   \n",
       "SEPT10P1                                        1.047   \n",
       "\n",
       "           Calu3_polyA_series1-S1-24h-B  \\\n",
       "genes                                     \n",
       "ETV5-AS1                          0.000   \n",
       "LINC01299                         0.000   \n",
       "MLLT3                             6.875   \n",
       "SCGB3A2                           0.000   \n",
       "SEPT10P1                          1.172   \n",
       "\n",
       "           Calu3_polyA_series1-S1-24h-B-detachedcells  \\\n",
       "genes                                                   \n",
       "ETV5-AS1                                        0.000   \n",
       "LINC01299                                       0.000   \n",
       "MLLT3                                           9.475   \n",
       "SCGB3A2                                         0.000   \n",
       "SEPT10P1                                        1.977   \n",
       "\n",
       "           Calu3_polyA_series1-S2-4h-A  Calu3_polyA_series1-S2-4h-B  ...  \\\n",
       "genes                                                                ...   \n",
       "ETV5-AS1                         0.000                        0.000  ...   \n",
       "LINC01299                        0.000                        0.029  ...   \n",
       "MLLT3                            4.435                        4.974  ...   \n",
       "SCGB3A2                          0.000                        0.000  ...   \n",
       "SEPT10P1                         1.259                        0.733  ...   \n",
       "\n",
       "           H1299_polyA_S2-24h-A  H1299_polyA_S2-24h-B  H1299_polyA_S2-36h-A  \\\n",
       "genes                                                                         \n",
       "ETV5-AS1                  0.000                 0.000                 0.000   \n",
       "LINC01299                 0.000                 0.000                 0.000   \n",
       "MLLT3                     4.287                 4.033                 3.814   \n",
       "SCGB3A2                   0.000                 0.000                 0.000   \n",
       "SEPT10P1                  2.090                 1.429                 1.462   \n",
       "\n",
       "           H1299_polyA_S2-36h-B  H1299_polyA_mock-4h-A  H1299_polyA_mock-4h-B  \\\n",
       "genes                                                                           \n",
       "ETV5-AS1                  0.000                  0.000                  0.000   \n",
       "LINC01299                 0.000                  0.000                  0.000   \n",
       "MLLT3                     3.549                  3.750                  3.820   \n",
       "SCGB3A2                   0.000                  0.000                  0.000   \n",
       "SEPT10P1                  1.729                  1.867                  1.586   \n",
       "\n",
       "           H1299_polyA_mock-36h-A  H1299_polyA_mock-36h-B  \\\n",
       "genes                                                       \n",
       "ETV5-AS1                    0.000                   0.000   \n",
       "LINC01299                   0.000                   0.000   \n",
       "MLLT3                       3.970                   4.311   \n",
       "SCGB3A2                     0.000                   0.000   \n",
       "SEPT10P1                    2.387                   2.268   \n",
       "\n",
       "           H1299_polyA_untr-4h-A  H1299_polyA_untr-4h-B  \n",
       "genes                                                    \n",
       "ETV5-AS1                   0.000                  0.000  \n",
       "LINC01299                  0.000                  0.000  \n",
       "MLLT3                      4.081                  3.734  \n",
       "SCGB3A2                    0.000                  0.000  \n",
       "SEPT10P1                   2.350                  1.254  \n",
       "\n",
       "[5 rows x 60 columns]"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['Calu3_polyA_series1-S1-4h-A', 'Calu3_polyA_series1-S1-4h-B',\n",
       "       'Calu3_polyA_series1-S1-12h-A', 'Calu3_polyA_series1-S1-12h-B',\n",
       "       'Calu3_polyA_series1-S1-24h-A',\n",
       "       'Calu3_polyA_series1-S1-24h-A-detachedcells',\n",
       "       'Calu3_polyA_series1-S1-24h-B',\n",
       "       'Calu3_polyA_series1-S1-24h-B-detachedcells',\n",
       "       'Calu3_polyA_series1-S2-4h-A', 'Calu3_polyA_series1-S2-4h-B',\n",
       "       'Calu3_polyA_series1-S2-12h-A', 'Calu3_polyA_series1-S2-12h-B',\n",
       "       'Calu3_polyA_series1-S2-24h-A',\n",
       "       'Calu3_polyA_series1-S2-24h-A-detachedcells',\n",
       "       'Calu3_polyA_series1-S2-24h-B',\n",
       "       'Calu3_polyA_series1-S2-24h-B-detachedcells',\n",
       "       'Calu3_polyA_series1-mock-4h-A', 'Calu3_polyA_series1-mock-4h-B',\n",
       "       'Calu3_polyA_series1-mock-24h-A', 'Calu3_polyA_series1-mock-24h-B',\n",
       "       'Calu3_polyA_series1-untr-4h-A', 'Calu3_polyA_series1-untr-4h-B',\n",
       "       'Calu3_polyA_series2-4h-S1-1', 'Calu3_polyA_series2-4h-S1-2',\n",
       "       'Calu3_polyA_series2-4h-S2-1', 'Calu3_polyA_series2-4h-S2-2',\n",
       "       'Calu3_polyA_series2-4h-mock-1', 'Calu3_polyA_series2-4h-mock-2',\n",
       "       'Calu3_polyA_series2-8h-S1-1', 'Calu3_polyA_series2-8h-S1-2',\n",
       "       'Calu3_polyA_series2-8h-S2-1', 'Calu3_polyA_series2-8h-S2-2',\n",
       "       'Calu3_polyA_series2-12h-S1-1', 'Calu3_polyA_series2-12h-S1-2',\n",
       "       'Calu3_polyA_series2-12h-S2-1', 'Calu3_polyA_series2-12h-S2-2',\n",
       "       'Calu3_polyA_series2-12h-mock-1', 'Calu3_polyA_series2-12h-mock-2',\n",
       "       'H1299_polyA_S1-4h-A', 'H1299_polyA_S1-4h-B', 'H1299_polyA_S1-12h-A',\n",
       "       'H1299_polyA_S1-12h-B', 'H1299_polyA_S1-24h-A', 'H1299_polyA_S1-24h-B',\n",
       "       'H1299_polyA_S1-36h-A', 'H1299_polyA_S1-36h-B', 'H1299_polyA_S2-4h-A',\n",
       "       'H1299_polyA_S2-4h-B', 'H1299_polyA_S2-12h-A', 'H1299_polyA_S2-12h-B',\n",
       "       'H1299_polyA_S2-24h-A', 'H1299_polyA_S2-24h-B', 'H1299_polyA_S2-36h-A',\n",
       "       'H1299_polyA_S2-36h-B', 'H1299_polyA_mock-4h-A',\n",
       "       'H1299_polyA_mock-4h-B', 'H1299_polyA_mock-36h-A',\n",
       "       'H1299_polyA_mock-36h-B', 'H1299_polyA_untr-4h-A',\n",
       "       'H1299_polyA_untr-4h-B'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'44'"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x = 'H1299_polyA_untr-44h-B'\n",
    "x[x.find('h-')-3 :x.find('h-')].split('-')[1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "meta = pd.DataFrame()\n",
    "meta['filename'] = df.columns\n",
    "#remove SARS1 smaples\n",
    "meta = meta.loc[~meta.filename.str.contains('S1'),:]\n",
    "meta = meta.loc[~meta.filename.str.contains('untr'),:]\n",
    "meta = meta.loc[~meta.filename.str.contains('detached'),:]\n",
    "\n",
    "meta['Cell_Line'] = meta['filename'].apply(lambda x:x.split('_')[0])\n",
    "#meta['phenotype'] = meta['filename'].apply(lambda x :'_'.join(x.split('_')[-1].split('-')[:-1]))\n",
    "\n",
    "meta['Time_Point'] = meta['filename'].apply(lambda x:x[x.find('h-')-3 :x.find('h-')].split('-')[1])\n",
    "#meta['Series'] = meta['filename'].apply(lambda x:x[x.find('polyA_'):x.find('polyA_')+15].split('-')[0].split('_')[1])\n",
    "#meta['SARS_CoV'] = meta['filename'].apply(lambda x:x[x.find('_S'):x.find('_S')+1].split('_')[0])\n",
    "#meta['detachedcells'] = meta['filename'].apply(lambda x:x.find('detachedcells'))\n",
    "meta['Phenotype'] = meta.Cell_Line +'_' +meta.Time_Point.astype('str')+'h'\n",
    "meta['Mock'] = meta['filename'].apply(lambda x:x.find('mock'))\n",
    "meta.loc[meta.Mock>-1,'Mock']= 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>filename</th>\n",
       "      <th>Cell_Line</th>\n",
       "      <th>Time_Point</th>\n",
       "      <th>Phenotype</th>\n",
       "      <th>Mock</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Calu3_polyA_series1-S2-4h-A</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>4</td>\n",
       "      <td>Calu3_4h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>Calu3_polyA_series1-S2-4h-B</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>4</td>\n",
       "      <td>Calu3_4h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>Calu3_polyA_series1-S2-12h-A</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>12</td>\n",
       "      <td>Calu3_12h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>Calu3_polyA_series1-S2-12h-B</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>12</td>\n",
       "      <td>Calu3_12h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Calu3_polyA_series1-S2-24h-A</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>24</td>\n",
       "      <td>Calu3_24h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>Calu3_polyA_series1-S2-24h-B</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>24</td>\n",
       "      <td>Calu3_24h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>Calu3_polyA_series1-mock-4h-A</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>4</td>\n",
       "      <td>Calu3_4h</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>Calu3_polyA_series1-mock-4h-B</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>4</td>\n",
       "      <td>Calu3_4h</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>Calu3_polyA_series1-mock-24h-A</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>24</td>\n",
       "      <td>Calu3_24h</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>Calu3_polyA_series1-mock-24h-B</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>24</td>\n",
       "      <td>Calu3_24h</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>Calu3_polyA_series2-4h-S2-1</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>4</td>\n",
       "      <td>Calu3_4h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>Calu3_polyA_series2-4h-S2-2</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>4</td>\n",
       "      <td>Calu3_4h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>Calu3_polyA_series2-4h-mock-1</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>4</td>\n",
       "      <td>Calu3_4h</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>Calu3_polyA_series2-4h-mock-2</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>4</td>\n",
       "      <td>Calu3_4h</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>Calu3_polyA_series2-8h-S2-1</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>8</td>\n",
       "      <td>Calu3_8h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>Calu3_polyA_series2-8h-S2-2</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>8</td>\n",
       "      <td>Calu3_8h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>Calu3_polyA_series2-12h-S2-1</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>12</td>\n",
       "      <td>Calu3_12h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>Calu3_polyA_series2-12h-S2-2</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>12</td>\n",
       "      <td>Calu3_12h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>Calu3_polyA_series2-12h-mock-1</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>12</td>\n",
       "      <td>Calu3_12h</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>Calu3_polyA_series2-12h-mock-2</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>12</td>\n",
       "      <td>Calu3_12h</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>H1299_polyA_S2-4h-A</td>\n",
       "      <td>H1299</td>\n",
       "      <td>4</td>\n",
       "      <td>H1299_4h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>H1299_polyA_S2-4h-B</td>\n",
       "      <td>H1299</td>\n",
       "      <td>4</td>\n",
       "      <td>H1299_4h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>H1299_polyA_S2-12h-A</td>\n",
       "      <td>H1299</td>\n",
       "      <td>12</td>\n",
       "      <td>H1299_12h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>49</th>\n",
       "      <td>H1299_polyA_S2-12h-B</td>\n",
       "      <td>H1299</td>\n",
       "      <td>12</td>\n",
       "      <td>H1299_12h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>50</th>\n",
       "      <td>H1299_polyA_S2-24h-A</td>\n",
       "      <td>H1299</td>\n",
       "      <td>24</td>\n",
       "      <td>H1299_24h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>51</th>\n",
       "      <td>H1299_polyA_S2-24h-B</td>\n",
       "      <td>H1299</td>\n",
       "      <td>24</td>\n",
       "      <td>H1299_24h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52</th>\n",
       "      <td>H1299_polyA_S2-36h-A</td>\n",
       "      <td>H1299</td>\n",
       "      <td>36</td>\n",
       "      <td>H1299_36h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>53</th>\n",
       "      <td>H1299_polyA_S2-36h-B</td>\n",
       "      <td>H1299</td>\n",
       "      <td>36</td>\n",
       "      <td>H1299_36h</td>\n",
       "      <td>-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>54</th>\n",
       "      <td>H1299_polyA_mock-4h-A</td>\n",
       "      <td>H1299</td>\n",
       "      <td>4</td>\n",
       "      <td>H1299_4h</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55</th>\n",
       "      <td>H1299_polyA_mock-4h-B</td>\n",
       "      <td>H1299</td>\n",
       "      <td>4</td>\n",
       "      <td>H1299_4h</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56</th>\n",
       "      <td>H1299_polyA_mock-36h-A</td>\n",
       "      <td>H1299</td>\n",
       "      <td>36</td>\n",
       "      <td>H1299_36h</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>57</th>\n",
       "      <td>H1299_polyA_mock-36h-B</td>\n",
       "      <td>H1299</td>\n",
       "      <td>36</td>\n",
       "      <td>H1299_36h</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                          filename Cell_Line Time_Point  Phenotype  Mock\n",
       "8      Calu3_polyA_series1-S2-4h-A     Calu3          4   Calu3_4h    -1\n",
       "9      Calu3_polyA_series1-S2-4h-B     Calu3          4   Calu3_4h    -1\n",
       "10    Calu3_polyA_series1-S2-12h-A     Calu3         12  Calu3_12h    -1\n",
       "11    Calu3_polyA_series1-S2-12h-B     Calu3         12  Calu3_12h    -1\n",
       "12    Calu3_polyA_series1-S2-24h-A     Calu3         24  Calu3_24h    -1\n",
       "14    Calu3_polyA_series1-S2-24h-B     Calu3         24  Calu3_24h    -1\n",
       "16   Calu3_polyA_series1-mock-4h-A     Calu3          4   Calu3_4h     1\n",
       "17   Calu3_polyA_series1-mock-4h-B     Calu3          4   Calu3_4h     1\n",
       "18  Calu3_polyA_series1-mock-24h-A     Calu3         24  Calu3_24h     1\n",
       "19  Calu3_polyA_series1-mock-24h-B     Calu3         24  Calu3_24h     1\n",
       "24     Calu3_polyA_series2-4h-S2-1     Calu3          4   Calu3_4h    -1\n",
       "25     Calu3_polyA_series2-4h-S2-2     Calu3          4   Calu3_4h    -1\n",
       "26   Calu3_polyA_series2-4h-mock-1     Calu3          4   Calu3_4h     1\n",
       "27   Calu3_polyA_series2-4h-mock-2     Calu3          4   Calu3_4h     1\n",
       "30     Calu3_polyA_series2-8h-S2-1     Calu3          8   Calu3_8h    -1\n",
       "31     Calu3_polyA_series2-8h-S2-2     Calu3          8   Calu3_8h    -1\n",
       "34    Calu3_polyA_series2-12h-S2-1     Calu3         12  Calu3_12h    -1\n",
       "35    Calu3_polyA_series2-12h-S2-2     Calu3         12  Calu3_12h    -1\n",
       "36  Calu3_polyA_series2-12h-mock-1     Calu3         12  Calu3_12h     1\n",
       "37  Calu3_polyA_series2-12h-mock-2     Calu3         12  Calu3_12h     1\n",
       "46             H1299_polyA_S2-4h-A     H1299          4   H1299_4h    -1\n",
       "47             H1299_polyA_S2-4h-B     H1299          4   H1299_4h    -1\n",
       "48            H1299_polyA_S2-12h-A     H1299         12  H1299_12h    -1\n",
       "49            H1299_polyA_S2-12h-B     H1299         12  H1299_12h    -1\n",
       "50            H1299_polyA_S2-24h-A     H1299         24  H1299_24h    -1\n",
       "51            H1299_polyA_S2-24h-B     H1299         24  H1299_24h    -1\n",
       "52            H1299_polyA_S2-36h-A     H1299         36  H1299_36h    -1\n",
       "53            H1299_polyA_S2-36h-B     H1299         36  H1299_36h    -1\n",
       "54           H1299_polyA_mock-4h-A     H1299          4   H1299_4h     1\n",
       "55           H1299_polyA_mock-4h-B     H1299          4   H1299_4h     1\n",
       "56          H1299_polyA_mock-36h-A     H1299         36  H1299_36h     1\n",
       "57          H1299_polyA_mock-36h-B     H1299         36  H1299_36h     1"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "meta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Phenotype</th>\n",
       "      <th>Cell_Line</th>\n",
       "      <th>Time_Point</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Calu3_4h</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>Calu3_12h</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Calu3_24h</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>24</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>Calu3_8h</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>H1299_4h</td>\n",
       "      <td>H1299</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>H1299_12h</td>\n",
       "      <td>H1299</td>\n",
       "      <td>12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>50</th>\n",
       "      <td>H1299_24h</td>\n",
       "      <td>H1299</td>\n",
       "      <td>24</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52</th>\n",
       "      <td>H1299_36h</td>\n",
       "      <td>H1299</td>\n",
       "      <td>36</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    Phenotype Cell_Line Time_Point\n",
       "8    Calu3_4h     Calu3          4\n",
       "10  Calu3_12h     Calu3         12\n",
       "12  Calu3_24h     Calu3         24\n",
       "30   Calu3_8h     Calu3          8\n",
       "46   H1299_4h     H1299          4\n",
       "48  H1299_12h     H1299         12\n",
       "50  H1299_24h     H1299         24\n",
       "52  H1299_36h     H1299         36"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "meta.loc[:,['Phenotype','Cell_Line','Time_Point']].drop_duplicates()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "    .dataframe tbody tr th:only-of-type {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>filename</th>\n",
       "      <th>Cell_Line</th>\n",
       "      <th>Time_Point</th>\n",
       "      <th>Phenotype</th>\n",
       "      <th>Mock</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Calu3_polyA_series1-S2-4h-A</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>4</td>\n",
       "      <td>Calu3_4h</td>\n",
       "      <td>Infected</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>Calu3_polyA_series1-S2-4h-B</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>4</td>\n",
       "      <td>Calu3_4h</td>\n",
       "      <td>Infected</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>Calu3_polyA_series1-S2-12h-A</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>12</td>\n",
       "      <td>Calu3_12h</td>\n",
       "      <td>Infected</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>Calu3_polyA_series1-S2-12h-B</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>12</td>\n",
       "      <td>Calu3_12h</td>\n",
       "      <td>Infected</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Calu3_polyA_series1-S2-24h-A</td>\n",
       "      <td>Calu3</td>\n",
       "      <td>24</td>\n",
       "      <td>Calu3_24h</td>\n",
       "      <td>Infected</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                        filename Cell_Line Time_Point  Phenotype      Mock\n",
       "8    Calu3_polyA_series1-S2-4h-A     Calu3          4   Calu3_4h  Infected\n",
       "9    Calu3_polyA_series1-S2-4h-B     Calu3          4   Calu3_4h  Infected\n",
       "10  Calu3_polyA_series1-S2-12h-A     Calu3         12  Calu3_12h  Infected\n",
       "11  Calu3_polyA_series1-S2-12h-B     Calu3         12  Calu3_12h  Infected\n",
       "12  Calu3_polyA_series1-S2-24h-A     Calu3         24  Calu3_24h  Infected"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "meta.loc[meta['Mock']==1,'Mock']  = 'Mock' \n",
    "meta.loc[meta['Mock']==-1,'Mock']  = 'Infected' \n",
    "meta.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Calu3_4h     8\n",
       "Calu3_12h    6\n",
       "Calu3_24h    4\n",
       "H1299_4h     4\n",
       "H1299_36h    4\n",
       "Calu3_8h     2\n",
       "H1299_24h    2\n",
       "H1299_12h    2\n",
       "Name: Phenotype, dtype: int64"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "meta.Phenotype.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Infected    20\n",
       "Mock        12\n",
       "Name: Mock, dtype: int64"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "meta.Mock.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Calu3_4h_Infected     4\n",
       "Calu3_12h_Infected    4\n",
       "Calu3_4h_Mock         4\n",
       "Calu3_8h_Infected     2\n",
       "Calu3_24h_Mock        2\n",
       "Calu3_12h_Mock        2\n",
       "H1299_24h_Infected    2\n",
       "H1299_36h_Infected    2\n",
       "H1299_4h_Mock         2\n",
       "H1299_12h_Infected    2\n",
       "H1299_36h_Mock        2\n",
       "H1299_4h_Infected     2\n",
       "Calu3_24h_Infected    2\n",
       "Name: Phenotype_Mock, dtype: int64"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "meta['Phenotype_Mock'] = meta['Phenotype']+'_'+meta['Mock'].astype('str')\n",
    "meta['Phenotype_Mock'].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [],
   "source": [
    "meta.to_csv('data/time_series_study/metadata.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "if not os.path.exists('data/time_series_study/FPKM_divided/'):\n",
    "    os.makedirs('data/time_series_study/FPKM_divided/')\n",
    "phenotypes = meta.Phenotype.unique().tolist()\n",
    "for i in phenotypes:\n",
    "    files = meta.loc[meta.Phenotype==i,'filename']\n",
    "    healthy_files = [x for x in files if x.find('mock') =='Mock']\n",
    "    infected_files = [x for x in files if x.find('mock') == 'Infected']\n",
    "    df.loc[:,files].to_csv('data/time_series_study/FPKM_divided/'+i+'.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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