YKO_library.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "from matplotlib import pyplot as plt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Process YKO library"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [],
   "source": [
    "table_path='/Users/paucac/Documents/PhD/CAB/CRISPA/YKO_library/'\n",
    "col_names=['Plate', 'Row','Column','ORF','Gene','Description','GO Biological Process','GO Molecular Function','GO Cellular Component','96-position']\n",
    "Data = pd.read_csv(table_path+ '384format.csv', delimiter=';', names=col_names, skiprows=2)\n",
    "Data = Data.drop('96-position', 1)\n",
    "Data.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "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>Plate</th>\n",
       "      <th>Row</th>\n",
       "      <th>Column</th>\n",
       "      <th>ORF</th>\n",
       "      <th>Gene</th>\n",
       "      <th>Description</th>\n",
       "      <th>GO Biological Process</th>\n",
       "      <th>GO Molecular Function</th>\n",
       "      <th>GO Cellular Component</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>1</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>2</td>\n",
       "      <td>YLL040C</td>\n",
       "      <td>VPS13</td>\n",
       "      <td>Protein of unknown function; heterooligomeric ...</td>\n",
       "      <td>transport, sporulation resulting in formation ...</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>mitochondrion, membrane, cytoplasm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>3</td>\n",
       "      <td>YAL068C</td>\n",
       "      <td>PAU8</td>\n",
       "      <td>Protein of unknown function, member of the ser...</td>\n",
       "      <td>sporulation resulting in formation of a cellul...</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>cellular_component</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>4</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>5</td>\n",
       "      <td>YAL067C</td>\n",
       "      <td>SEO1</td>\n",
       "      <td>Putative permease, member of the allantoate tr...</td>\n",
       "      <td>transport</td>\n",
       "      <td>transporter activity</td>\n",
       "      <td>membrane</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   Plate Row  Column      ORF   Gene  \\\n",
       "0      1   A       1    Blank  Blank   \n",
       "1      1   A       2  YLL040C  VPS13   \n",
       "2      1   A       3  YAL068C   PAU8   \n",
       "3      1   A       4    Blank  Blank   \n",
       "4      1   A       5  YAL067C   SEO1   \n",
       "\n",
       "                                         Description  \\\n",
       "0                                              Blank   \n",
       "1  Protein of unknown function; heterooligomeric ...   \n",
       "2  Protein of unknown function, member of the ser...   \n",
       "3                                              Blank   \n",
       "4  Putative permease, member of the allantoate tr...   \n",
       "\n",
       "                               GO Biological Process GO Molecular Function  \\\n",
       "0                                              Blank                 Blank   \n",
       "1  transport, sporulation resulting in formation ...    molecular_function   \n",
       "2  sporulation resulting in formation of a cellul...    molecular_function   \n",
       "3                                              Blank                 Blank   \n",
       "4                                          transport  transporter activity   \n",
       "\n",
       "                GO Cellular Component  \n",
       "0                               Blank  \n",
       "1  mitochondrion, membrane, cytoplasm  \n",
       "2                  cellular_component  \n",
       "3                               Blank  \n",
       "4                            membrane  "
      ]
     },
     "execution_count": 44,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "384"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "8*2*12*2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "letter={'A':1,\n",
    "        'B':2,\n",
    "        'C':3,\n",
    "        'D':4,\n",
    "        'E':5,\n",
    "        'F':6,\n",
    "        'G':7,\n",
    "        'H':8,\n",
    "        'I':9,\n",
    "        'J':10,\n",
    "        'K':11,\n",
    "        'L':12,\n",
    "        'M':13,\n",
    "        'N':14,\n",
    "        'O':15,\n",
    "        'P':16\n",
    "        \n",
    "       }\n",
    "number={}\n",
    "\n",
    "for L,N in letter.items():\n",
    "    number[N]=L"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [],
   "source": [
    "plates384={}\n",
    "for i in range(1,14):\n",
    "    plates384[i]=np.empty([16,24])\n",
    "    \n",
    "for i in range(len(Data)):\n",
    "    P=Data['Plate'].iloc[i] \n",
    "    R=letter[Data['Row'].iloc[i]] -1\n",
    "    C = Data['Column'].iloc[i] -1\n",
    "    plates384[P][R,C] = int(i)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [],
   "source": [
    "#when replicating the YKO library96well plates were arranged in the following configuration:\n",
    "#    Red:plateA    Blue:plateB\n",
    "#.   Yellow: PlateC Green:plateD\n",
    "\n",
    "plates96={}\n",
    "for i in range(1,13+1):\n",
    "        plates96['A'+str(i)]=plates384[i][::2,::2]\n",
    "        plates96['B'+str(i)]=plates384[i][::2,1::2]\n",
    "        plates96['C'+str(i)]=plates384[i][1::2,::2]\n",
    "        plates96['D'+str(i)]=plates384[i][1::2,1::2]\n",
    "        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['YLL046C', 'RNP1',\n",
       "       'Ribonucleoprotein that contains two RNA recognition motifs (RRM)',\n",
       "       'ribosome biogenesis', 'RNA binding', 'cytoplasm'], dtype=object)"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Data.iloc[i].values[3:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 181,
   "metadata": {},
   "outputs": [],
   "source": [
    "Data96=[]\n",
    "i=0\n",
    "for P in range(1,13+1):\n",
    "    for L in ['A','B','C','D']:\n",
    "        for row in range(1,9):\n",
    "            for col in range(1,13):\n",
    "                i= int(plates96[L+str(P)][row-1][col-1])\n",
    "                new_line= [str(P)+L,number[row], col]\n",
    "                [new_line.append(cell) for cell in list( Data.iloc[i].values[3:])]\n",
    "                #print(new_line)\n",
    "                Data96.append(new_line)\n",
    "               # i+=1\n",
    "        \n",
    "Data96=np.vstack(Data96)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 173,
   "metadata": {},
   "outputs": [],
   "source": [
    "gene_plate =plates96['A1'].copy()\n",
    "gene_plate = (gene_plate*0).astype(str)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 174,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<matplotlib.image.AxesImage at 0x11e6c3950>"
      ]
     },
     "execution_count": 174,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "#check that plate blank spots match pictures\n",
    "plate='C9'\n",
    "for r in range(8):\n",
    "    for c in range(12):\n",
    "        i=plates96[plate][r,c]\n",
    "        gene_plate[r,c]= Data['Gene'].iloc[int(i)]\n",
    "        \n",
    "plt.imshow(gene_plate=='Blank')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'CHO2'"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "plate='B4'\n",
    "row=0\n",
    "col=2\n",
    "i=plates96[plate][row,col]\n",
    "Data['Gene'].iloc[int(i)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 175,
   "metadata": {},
   "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>Plate</th>\n",
       "      <th>Row</th>\n",
       "      <th>Column</th>\n",
       "      <th>ORF</th>\n",
       "      <th>Gene</th>\n",
       "      <th>Description</th>\n",
       "      <th>GO Biological Process</th>\n",
       "      <th>GO Molecular Function</th>\n",
       "      <th>GO Cellular Component</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1A</td>\n",
       "      <td>A</td>\n",
       "      <td>1</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1A</td>\n",
       "      <td>A</td>\n",
       "      <td>2</td>\n",
       "      <td>YAL068C</td>\n",
       "      <td>PAU8</td>\n",
       "      <td>Protein of unknown function, member of the ser...</td>\n",
       "      <td>sporulation resulting in formation of a cellul...</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>cellular_component</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1A</td>\n",
       "      <td>A</td>\n",
       "      <td>3</td>\n",
       "      <td>YAL067C</td>\n",
       "      <td>SEO1</td>\n",
       "      <td>Putative permease, member of the allantoate tr...</td>\n",
       "      <td>transport</td>\n",
       "      <td>transporter activity</td>\n",
       "      <td>membrane</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1A</td>\n",
       "      <td>A</td>\n",
       "      <td>4</td>\n",
       "      <td>YAL066W</td>\n",
       "      <td>YAL066W</td>\n",
       "      <td>Dubious open reading frame unlikely to encode ...</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>cellular_component</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1A</td>\n",
       "      <td>A</td>\n",
       "      <td>5</td>\n",
       "      <td>YAL065C</td>\n",
       "      <td>YAL065C</td>\n",
       "      <td>Putative protein of unknown function; has homo...</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>cellular_component</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4984</th>\n",
       "      <td>13D</td>\n",
       "      <td>H</td>\n",
       "      <td>5</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4985</th>\n",
       "      <td>13D</td>\n",
       "      <td>H</td>\n",
       "      <td>6</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4986</th>\n",
       "      <td>13D</td>\n",
       "      <td>H</td>\n",
       "      <td>7</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4987</th>\n",
       "      <td>13D</td>\n",
       "      <td>H</td>\n",
       "      <td>8</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4988</th>\n",
       "      <td>13D</td>\n",
       "      <td>H</td>\n",
       "      <td>9</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4989 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     Plate Row Column      ORF     Gene  \\\n",
       "0       1A   A      1    Blank    Blank   \n",
       "1       1A   A      2  YAL068C     PAU8   \n",
       "2       1A   A      3  YAL067C     SEO1   \n",
       "3       1A   A      4  YAL066W  YAL066W   \n",
       "4       1A   A      5  YAL065C  YAL065C   \n",
       "...    ...  ..    ...      ...      ...   \n",
       "4984   13D   H      5    Blank    Blank   \n",
       "4985   13D   H      6    Blank    Blank   \n",
       "4986   13D   H      7    Blank    Blank   \n",
       "4987   13D   H      8    Blank    Blank   \n",
       "4988   13D   H      9    Blank    Blank   \n",
       "\n",
       "                                            Description  \\\n",
       "0                                                 Blank   \n",
       "1     Protein of unknown function, member of the ser...   \n",
       "2     Putative permease, member of the allantoate tr...   \n",
       "3     Dubious open reading frame unlikely to encode ...   \n",
       "4     Putative protein of unknown function; has homo...   \n",
       "...                                                 ...   \n",
       "4984                                              Blank   \n",
       "4985                                              Blank   \n",
       "4986                                              Blank   \n",
       "4987                                              Blank   \n",
       "4988                                              Blank   \n",
       "\n",
       "                                  GO Biological Process GO Molecular Function  \\\n",
       "0                                                 Blank                 Blank   \n",
       "1     sporulation resulting in formation of a cellul...    molecular_function   \n",
       "2                                             transport  transporter activity   \n",
       "3                                    biological_process    molecular_function   \n",
       "4                                    biological_process    molecular_function   \n",
       "...                                                 ...                   ...   \n",
       "4984                                              Blank                 Blank   \n",
       "4985                                              Blank                 Blank   \n",
       "4986                                              Blank                 Blank   \n",
       "4987                                              Blank                 Blank   \n",
       "4988                                              Blank                 Blank   \n",
       "\n",
       "     GO Cellular Component  \n",
       "0                    Blank  \n",
       "1       cellular_component  \n",
       "2                 membrane  \n",
       "3       cellular_component  \n",
       "4       cellular_component  \n",
       "...                    ...  \n",
       "4984                 Blank  \n",
       "4985                 Blank  \n",
       "4986                 Blank  \n",
       "4987                 Blank  \n",
       "4988                 Blank  \n",
       "\n",
       "[4989 rows x 9 columns]"
      ]
     },
     "execution_count": 175,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Format96=pd.DataFrame(Data96, columns = list(Data.columns))\n",
    "\n",
    "Format96.head(-3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 187,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Gene      SDH2\n",
      "Plate        1\n",
      "Row          A\n",
      "Column       6\n",
      "Name: 5, dtype: object\n",
      "    Gene Plate Row Column\n",
      "98  SDH2    1B   A      3\n"
     ]
    }
   ],
   "source": [
    "i=5\n",
    "print(Data[['Gene','Plate', 'Row','Column']].iloc[i])\n",
    "gene=Data['Gene'].iloc[i]\n",
    "new_i=np.where(Format96['Gene']==gene)[0]\n",
    "print(Format96[['Gene','Plate', 'Row','Column']].iloc[new_i])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [],
   "source": [
    "#we create a table with both format for benchling\n",
    "FormatBoth= Format96.copy()\n",
    "FormatBoth['Plate_96format'] = Format96['Plate']\n",
    "FormatBoth = FormatBoth.drop('Plate', 1)\n",
    "FormatBoth['Plate_384format'] = Data['Plate']\n",
    "#reorder columns \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [],
   "source": [
    "cols = FormatBoth.columns.tolist()\n",
    "cols =  cols[-2:] + cols[:-2]\n",
    "FormatBoth = FormatBoth[cols]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "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>Plate_96format</th>\n",
       "      <th>Plate_384format</th>\n",
       "      <th>Row</th>\n",
       "      <th>Column</th>\n",
       "      <th>ORF</th>\n",
       "      <th>Gene</th>\n",
       "      <th>Description</th>\n",
       "      <th>GO Biological Process</th>\n",
       "      <th>GO Molecular Function</th>\n",
       "      <th>GO Cellular Component</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1A</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>1</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1A</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>2</td>\n",
       "      <td>YLL040C</td>\n",
       "      <td>VPS13</td>\n",
       "      <td>Protein of unknown function; heterooligomeric ...</td>\n",
       "      <td>transport, sporulation resulting in formation ...</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>mitochondrion, membrane, cytoplasm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1A</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>3</td>\n",
       "      <td>YAL068C</td>\n",
       "      <td>PAU8</td>\n",
       "      <td>Protein of unknown function, member of the ser...</td>\n",
       "      <td>sporulation resulting in formation of a cellul...</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>cellular_component</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1A</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>4</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1A</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>5</td>\n",
       "      <td>YAL067C</td>\n",
       "      <td>SEO1</td>\n",
       "      <td>Putative permease, member of the allantoate tr...</td>\n",
       "      <td>transport</td>\n",
       "      <td>transporter activity</td>\n",
       "      <td>membrane</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  Plate_96format  Plate_384format Row Column      ORF   Gene  \\\n",
       "0             1A                1   A      1    Blank  Blank   \n",
       "1             1A                1   A      2  YLL040C  VPS13   \n",
       "2             1A                1   A      3  YAL068C   PAU8   \n",
       "3             1A                1   A      4    Blank  Blank   \n",
       "4             1A                1   A      5  YAL067C   SEO1   \n",
       "\n",
       "                                         Description  \\\n",
       "0                                              Blank   \n",
       "1  Protein of unknown function; heterooligomeric ...   \n",
       "2  Protein of unknown function, member of the ser...   \n",
       "3                                              Blank   \n",
       "4  Putative permease, member of the allantoate tr...   \n",
       "\n",
       "                               GO Biological Process GO Molecular Function  \\\n",
       "0                                              Blank                 Blank   \n",
       "1  transport, sporulation resulting in formation ...    molecular_function   \n",
       "2  sporulation resulting in formation of a cellul...    molecular_function   \n",
       "3                                              Blank                 Blank   \n",
       "4                                          transport  transporter activity   \n",
       "\n",
       "                GO Cellular Component  \n",
       "0                               Blank  \n",
       "1  mitochondrion, membrane, cytoplasm  \n",
       "2                  cellular_component  \n",
       "3                               Blank  \n",
       "4                            membrane  "
      ]
     },
     "execution_count": 57,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "FormatBoth.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [],
   "source": [
    "#save FormatBoth\n",
    "FormatBoth.to_csv(table_path+'Bencnling_Entry.csv', sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "metadata": {},
   "outputs": [],
   "source": [
    "#save as csv tables\n",
    "Format96.to_csv(table_path+'Format96.csv', sep='\\t')\n",
    "Data.to_csv(table_path+'Format384.csv', sep='\\t')\n",
    "\n",
    "\n",
    "#write a read_me file:\n",
    "read_me = open(table_path+'Read_Me.txt', 'w')\n",
    "corpus= 'YKO library\\n\\n\\n'\n",
    "corpus+='For Details refer to Giaever et al. 2002 ( doi:10.1038/nature00935 )\\n\\n'\n",
    "corpus+='Gene Emplacement in:\\n Format96.csv and Format384.csv (tab delimited) \\n'\n",
    "corpus+=\"Files contain: [Plate, Row, Column, ORF, Gene, Decription, GO Biological Process, GO Molecular Function, GO Cellular Component]\\n\\n\"\n",
    "corpus+= 'Replication Procedure:\\n'\n",
    "corpus+='The YKO library was replicated in May 2021 by Paul Cachera (paucac@biosustain.dtu.dk) ' \n",
    "corpus+='The libary in 384 arrays on agar (provided by Michael Lisby mlisby@bio.ku.dk) was transferred (Singers Rotor) '\n",
    "corpus+='to 96well plates filled with 120microL YPD (Flowrobotics Flowbot1). The plates were incubated @30C for approx 48h. '\n",
    "corpus+='80uL of 50% glycerol was added to each well. Each well was mannually stirred with sterile Rotor pin pads'\n",
    "read_me.write(corpus)\n",
    "read_me.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "YKO library\n",
      "\n",
      "\n",
      "For Details refer to Giaever et al. 2002 ( doi:10.1038/nature00935 )\n",
      "\n",
      "Gene Emplacement in:\n",
      " Format96.csv and Format384.csv (tab delimited) \n",
      "Files contain: [Plate, Row, Column, ORF, Gene, Decription, GO Biological Process, GO Molecular Function, GO Cellular Component]\n",
      "\n",
      "Replication Procedure:\n",
      "The YKO library was replicated in May 2021 by Paul Cachera (paucac@biosustain.dtu.dk) The libary in 384 arrays on agar (provided by Michael Lisby mlisby@bio.ku.dk) was transferred (Singers Rotor) to 96well plates filled with 120microL YPD (Flowrobotics Flowbot1). The plates were incubated @30C for approx 48h. 80uL of 50% glycerol was added to each well. Each well was mannually stirred with sterile Rotor pin pads\n"
     ]
    }
   ],
   "source": [
    "print(corpus)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Process TS library"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "['Strain ID',,'ts allele','ts on SC','Background','Description','Genotype Mata','Plate','Row','Column','ORF','Gene','Decription','TS allele']\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 105,
   "metadata": {},
   "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>Strain ID</th>\n",
       "      <th>ts allele</th>\n",
       "      <th>ts on SC</th>\n",
       "      <th>Background</th>\n",
       "      <th>Description</th>\n",
       "      <th>Genotype Mata</th>\n",
       "      <th>Plate</th>\n",
       "      <th>Row</th>\n",
       "      <th>Column</th>\n",
       "      <th>ORF</th>\n",
       "      <th>Gene</th>\n",
       "      <th>Decription</th>\n",
       "      <th>TS allele</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>1</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>0</td>\n",
       "      <td>Blank</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TSA146</td>\n",
       "      <td>cdc14-3</td>\n",
       "      <td>Lethal at 26°C</td>\n",
       "      <td>BY4741</td>\n",
       "      <td>Protein phosphatase required for mitotic exit;...</td>\n",
       "      <td>cdc14-3::KanR;  his3^1 leu2^0 ura3^0 met15^0</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>2</td>\n",
       "      <td>YOR046C</td>\n",
       "      <td>DBP5</td>\n",
       "      <td>Cytoplasmic ATP-dependent RNA helicase of the ...</td>\n",
       "      <td>dbp5-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TSA198</td>\n",
       "      <td>sed5-1</td>\n",
       "      <td>Lethal at 26°C</td>\n",
       "      <td>BY4741</td>\n",
       "      <td>cis-Golgi t-SNARE syntaxin; required for vesic...</td>\n",
       "      <td>sed5-1::KanR;  his3^1 leu2^0 ura3^0 met15^0</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>3</td>\n",
       "      <td>YFR028C</td>\n",
       "      <td>CDC14</td>\n",
       "      <td>Protein phosphatase required for mitotic exit;...</td>\n",
       "      <td>cdc14-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>TSA920</td>\n",
       "      <td>gle1-4</td>\n",
       "      <td>Lethal at 26°C</td>\n",
       "      <td>BY4741</td>\n",
       "      <td>Cytoplasmic nucleoporin required for polyadeny...</td>\n",
       "      <td>gle1-4::KanR;  his3^1 leu2^0 ura3^0 met15^0</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>4</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Blank</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  Strain ID ts allele        ts on SC Background  \\\n",
       "0     Blank     Blank             NaN        NaN   \n",
       "1    TSA146   cdc14-3  Lethal at 26°C     BY4741   \n",
       "2    TSA198    sed5-1  Lethal at 26°C     BY4741   \n",
       "3    TSA920    gle1-4  Lethal at 26°C     BY4741   \n",
       "\n",
       "                                         Description  \\\n",
       "0                                                NaN   \n",
       "1  Protein phosphatase required for mitotic exit;...   \n",
       "2  cis-Golgi t-SNARE syntaxin; required for vesic...   \n",
       "3  Cytoplasmic nucleoporin required for polyadeny...   \n",
       "\n",
       "                                  Genotype Mata  Plate Row  Column      ORF  \\\n",
       "0                                           NaN      1   A       1    Blank   \n",
       "1  cdc14-3::KanR;  his3^1 leu2^0 ura3^0 met15^0      1   A       2  YOR046C   \n",
       "2   sed5-1::KanR;  his3^1 leu2^0 ura3^0 met15^0      1   A       3  YFR028C   \n",
       "3   gle1-4::KanR;  his3^1 leu2^0 ura3^0 met15^0      1   A       4    Blank   \n",
       "\n",
       "    Gene                                         Decription TS allele  \n",
       "0  Blank                                                  0     Blank  \n",
       "1   DBP5  Cytoplasmic ATP-dependent RNA helicase of the ...    dbp5-2  \n",
       "2  CDC14  Protein phosphatase required for mitotic exit;...   cdc14-3  \n",
       "3  Blank                                                NaN     Blank  "
      ]
     },
     "execution_count": 105,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "col_names=['Strain ID','Plate.','Row.','Col.','ORF.','Gene.','ts allele','ts on SC','Background','Description','Genotype Mata','Plate','Row','Column','ORF','Gene','Decription','TS allele']\n",
    "\n",
    "TS_384 = pd.read_csv(table_path+ 'TS_library.csv', names=col_names, delimiter=';', skiprows=1)\n",
    "TS_384 = TS_384.drop(['Plate.','Row.','Col.','ORF.','Gene.'], 1)\n",
    "TS_384.head(4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 94,
   "metadata": {},
   "outputs": [],
   "source": [
    "plates384TS={}\n",
    "for i in range(1,4):\n",
    "    plates384TS[i]=np.empty([16,24])\n",
    "    \n",
    "for i in range(len(TS_384)):\n",
    "    P=TS_384['Plate'].iloc[i] \n",
    "    R=letter[TS_384['Row'].iloc[i]] -1\n",
    "    C = TS_384['Column'].iloc[i] -1\n",
    "    plates384TS[P][R,C] = int(i)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 127,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(72.0, 72.0)"
      ]
     },
     "execution_count": 127,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "plate=1\n",
    "plates384TS[plate][3][0], plates96TS['D'+str(plate)][1][0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 97,
   "metadata": {},
   "outputs": [],
   "source": [
    "#when replicating the TS library96well plates were arranged in the following configuration:\n",
    "#    Red:plateA    Blue:plateB\n",
    "#.   Yellow:PlateD Green:plateC\n",
    "plates96TS={}\n",
    "for i in range(1,3+1):\n",
    "        plates96TS['A'+str(i)]=plates384TS[i][::2,::2]\n",
    "        plates96TS['B'+str(i)]=plates384TS[i][::2,1::2]\n",
    "        plates96TS['D'+str(i)]=plates384TS[i][1::2,::2]\n",
    "        plates96TS['C'+str(i)]=plates384TS[i][1::2,1::2]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 113,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "((1152, 11), 13)"
      ]
     },
     "execution_count": 113,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Data96TS.shape, len(list(TS_384.columns))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 139,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'A1': array([[  0.,   2.,   4.,   6.,   8.,  10.,  12.,  14.,  16.,  18.,  20.,\n",
       "          22.],\n",
       "        [ 48.,  50.,  52.,  54.,  56.,  58.,  60.,  62.,  64.,  66.,  68.,\n",
       "          70.],\n",
       "        [ 96.,  98., 100., 102., 104., 106., 108., 110., 112., 114., 116.,\n",
       "         118.],\n",
       "        [144., 146., 148., 150., 152., 154., 156., 158., 160., 162., 164.,\n",
       "         166.],\n",
       "        [192., 194., 196., 198., 200., 202., 204., 206., 208., 210., 212.,\n",
       "         214.],\n",
       "        [240., 242., 244., 246., 248., 250., 252., 254., 256., 258., 260.,\n",
       "         262.],\n",
       "        [288., 290., 292., 294., 296., 298., 300., 302., 304., 306., 308.,\n",
       "         310.],\n",
       "        [336., 338., 340., 342., 344., 346., 348., 350., 352., 354., 356.,\n",
       "         358.]]),\n",
       " 'B1': array([[  1.,   3.,   5.,   7.,   9.,  11.,  13.,  15.,  17.,  19.,  21.,\n",
       "          23.],\n",
       "        [ 49.,  51.,  53.,  55.,  57.,  59.,  61.,  63.,  65.,  67.,  69.,\n",
       "          71.],\n",
       "        [ 97.,  99., 101., 103., 105., 107., 109., 111., 113., 115., 117.,\n",
       "         119.],\n",
       "        [145., 147., 149., 151., 153., 155., 157., 159., 161., 163., 165.,\n",
       "         167.],\n",
       "        [193., 195., 197., 199., 201., 203., 205., 207., 209., 211., 213.,\n",
       "         215.],\n",
       "        [241., 243., 245., 247., 249., 251., 253., 255., 257., 259., 261.,\n",
       "         263.],\n",
       "        [289., 291., 293., 295., 297., 299., 301., 303., 305., 307., 309.,\n",
       "         311.],\n",
       "        [337., 339., 341., 343., 345., 347., 349., 351., 353., 355., 357.,\n",
       "         359.]]),\n",
       " 'D1': array([[ 24.,  26.,  28.,  30.,  32.,  34.,  36.,  38.,  40.,  42.,  44.,\n",
       "          46.],\n",
       "        [ 72.,  74.,  76.,  78.,  80.,  82.,  84.,  86.,  88.,  90.,  92.,\n",
       "          94.],\n",
       "        [120., 122., 124., 126., 128., 130., 132., 134., 136., 138., 140.,\n",
       "         142.],\n",
       "        [168., 170., 172., 174., 176., 178., 180., 182., 184., 186., 188.,\n",
       "         190.],\n",
       "        [216., 218., 220., 222., 224., 226., 228., 230., 232., 234., 236.,\n",
       "         238.],\n",
       "        [264., 266., 268., 270., 272., 274., 276., 278., 280., 282., 284.,\n",
       "         286.],\n",
       "        [312., 314., 316., 318., 320., 322., 324., 326., 328., 330., 332.,\n",
       "         334.],\n",
       "        [360., 362., 364., 366., 368., 370., 372., 374., 376., 378., 380.,\n",
       "         382.]]),\n",
       " 'C1': array([[ 25.,  27.,  29.,  31.,  33.,  35.,  37.,  39.,  41.,  43.,  45.,\n",
       "          47.],\n",
       "        [ 73.,  75.,  77.,  79.,  81.,  83.,  85.,  87.,  89.,  91.,  93.,\n",
       "          95.],\n",
       "        [121., 123., 125., 127., 129., 131., 133., 135., 137., 139., 141.,\n",
       "         143.],\n",
       "        [169., 171., 173., 175., 177., 179., 181., 183., 185., 187., 189.,\n",
       "         191.],\n",
       "        [217., 219., 221., 223., 225., 227., 229., 231., 233., 235., 237.,\n",
       "         239.],\n",
       "        [265., 267., 269., 271., 273., 275., 277., 279., 281., 283., 285.,\n",
       "         287.],\n",
       "        [313., 315., 317., 319., 321., 323., 325., 327., 329., 331., 333.,\n",
       "         335.],\n",
       "        [361., 363., 365., 367., 369., 371., 373., 375., 377., 379., 381.,\n",
       "         383.]]),\n",
       " 'A2': array([[384., 386., 388., 390., 392., 394., 396., 398., 400., 402., 404.,\n",
       "         406.],\n",
       "        [432., 434., 436., 438., 440., 442., 444., 446., 448., 450., 452.,\n",
       "         454.],\n",
       "        [480., 482., 484., 486., 488., 490., 492., 494., 496., 498., 500.,\n",
       "         502.],\n",
       "        [528., 530., 532., 534., 536., 538., 540., 542., 544., 546., 548.,\n",
       "         550.],\n",
       "        [576., 578., 580., 582., 584., 586., 588., 590., 592., 594., 596.,\n",
       "         598.],\n",
       "        [624., 626., 628., 630., 632., 634., 636., 638., 640., 642., 644.,\n",
       "         646.],\n",
       "        [672., 674., 676., 678., 680., 682., 684., 686., 688., 690., 692.,\n",
       "         694.],\n",
       "        [720., 722., 724., 726., 728., 730., 732., 734., 736., 738., 740.,\n",
       "         742.]]),\n",
       " 'B2': array([[385., 387., 389., 391., 393., 395., 397., 399., 401., 403., 405.,\n",
       "         407.],\n",
       "        [433., 435., 437., 439., 441., 443., 445., 447., 449., 451., 453.,\n",
       "         455.],\n",
       "        [481., 483., 485., 487., 489., 491., 493., 495., 497., 499., 501.,\n",
       "         503.],\n",
       "        [529., 531., 533., 535., 537., 539., 541., 543., 545., 547., 549.,\n",
       "         551.],\n",
       "        [577., 579., 581., 583., 585., 587., 589., 591., 593., 595., 597.,\n",
       "         599.],\n",
       "        [625., 627., 629., 631., 633., 635., 637., 639., 641., 643., 645.,\n",
       "         647.],\n",
       "        [673., 675., 677., 679., 681., 683., 685., 687., 689., 691., 693.,\n",
       "         695.],\n",
       "        [721., 723., 725., 727., 729., 731., 733., 735., 737., 739., 741.,\n",
       "         743.]]),\n",
       " 'D2': array([[408., 410., 412., 414., 416., 418., 420., 422., 424., 426., 428.,\n",
       "         430.],\n",
       "        [456., 458., 460., 462., 464., 466., 468., 470., 472., 474., 476.,\n",
       "         478.],\n",
       "        [504., 506., 508., 510., 512., 514., 516., 518., 520., 522., 524.,\n",
       "         526.],\n",
       "        [552., 554., 556., 558., 560., 562., 564., 566., 568., 570., 572.,\n",
       "         574.],\n",
       "        [600., 602., 604., 606., 608., 610., 612., 614., 616., 618., 620.,\n",
       "         622.],\n",
       "        [648., 650., 652., 654., 656., 658., 660., 662., 664., 666., 668.,\n",
       "         670.],\n",
       "        [696., 698., 700., 702., 704., 706., 708., 710., 712., 714., 716.,\n",
       "         718.],\n",
       "        [744., 746., 748., 750., 752., 754., 756., 758., 760., 762., 764.,\n",
       "         766.]]),\n",
       " 'C2': array([[409., 411., 413., 415., 417., 419., 421., 423., 425., 427., 429.,\n",
       "         431.],\n",
       "        [457., 459., 461., 463., 465., 467., 469., 471., 473., 475., 477.,\n",
       "         479.],\n",
       "        [505., 507., 509., 511., 513., 515., 517., 519., 521., 523., 525.,\n",
       "         527.],\n",
       "        [553., 555., 557., 559., 561., 563., 565., 567., 569., 571., 573.,\n",
       "         575.],\n",
       "        [601., 603., 605., 607., 609., 611., 613., 615., 617., 619., 621.,\n",
       "         623.],\n",
       "        [649., 651., 653., 655., 657., 659., 661., 663., 665., 667., 669.,\n",
       "         671.],\n",
       "        [697., 699., 701., 703., 705., 707., 709., 711., 713., 715., 717.,\n",
       "         719.],\n",
       "        [745., 747., 749., 751., 753., 755., 757., 759., 761., 763., 765.,\n",
       "         767.]]),\n",
       " 'A3': array([[ 768.,  770.,  772.,  774.,  776.,  778.,  780.,  782.,  784.,\n",
       "          786.,  788.,  790.],\n",
       "        [ 816.,  818.,  820.,  822.,  824.,  826.,  828.,  830.,  832.,\n",
       "          834.,  836.,  838.],\n",
       "        [ 864.,  866.,  868.,  870.,  872.,  874.,  876.,  878.,  880.,\n",
       "          882.,  884.,  886.],\n",
       "        [ 912.,  914.,  916.,  918.,  920.,  922.,  924.,  926.,  928.,\n",
       "          930.,  932.,  934.],\n",
       "        [ 960.,  962.,  964.,  966.,  968.,  970.,  972.,  974.,  976.,\n",
       "          978.,  980.,  982.],\n",
       "        [1008., 1010., 1012., 1014., 1016., 1018., 1020., 1022., 1024.,\n",
       "         1026., 1028., 1030.],\n",
       "        [1056., 1058., 1060., 1062., 1064., 1066., 1068., 1070., 1072.,\n",
       "         1074., 1076., 1078.],\n",
       "        [1104., 1106., 1108., 1110., 1112., 1114., 1116., 1118., 1120.,\n",
       "         1122., 1124., 1126.]]),\n",
       " 'B3': array([[ 769.,  771.,  773.,  775.,  777.,  779.,  781.,  783.,  785.,\n",
       "          787.,  789.,  791.],\n",
       "        [ 817.,  819.,  821.,  823.,  825.,  827.,  829.,  831.,  833.,\n",
       "          835.,  837.,  839.],\n",
       "        [ 865.,  867.,  869.,  871.,  873.,  875.,  877.,  879.,  881.,\n",
       "          883.,  885.,  887.],\n",
       "        [ 913.,  915.,  917.,  919.,  921.,  923.,  925.,  927.,  929.,\n",
       "          931.,  933.,  935.],\n",
       "        [ 961.,  963.,  965.,  967.,  969.,  971.,  973.,  975.,  977.,\n",
       "          979.,  981.,  983.],\n",
       "        [1009., 1011., 1013., 1015., 1017., 1019., 1021., 1023., 1025.,\n",
       "         1027., 1029., 1031.],\n",
       "        [1057., 1059., 1061., 1063., 1065., 1067., 1069., 1071., 1073.,\n",
       "         1075., 1077., 1079.],\n",
       "        [1105., 1107., 1109., 1111., 1113., 1115., 1117., 1119., 1121.,\n",
       "         1123., 1125., 1127.]]),\n",
       " 'D3': array([[ 792.,  794.,  796.,  798.,  800.,  802.,  804.,  806.,  808.,\n",
       "          810.,  812.,  814.],\n",
       "        [ 840.,  842.,  844.,  846.,  848.,  850.,  852.,  854.,  856.,\n",
       "          858.,  860.,  862.],\n",
       "        [ 888.,  890.,  892.,  894.,  896.,  898.,  900.,  902.,  904.,\n",
       "          906.,  908.,  910.],\n",
       "        [ 936.,  938.,  940.,  942.,  944.,  946.,  948.,  950.,  952.,\n",
       "          954.,  956.,  958.],\n",
       "        [ 984.,  986.,  988.,  990.,  992.,  994.,  996.,  998., 1000.,\n",
       "         1002., 1004., 1006.],\n",
       "        [1032., 1034., 1036., 1038., 1040., 1042., 1044., 1046., 1048.,\n",
       "         1050., 1052., 1054.],\n",
       "        [1080., 1082., 1084., 1086., 1088., 1090., 1092., 1094., 1096.,\n",
       "         1098., 1100., 1102.],\n",
       "        [1128., 1130., 1132., 1134., 1136., 1138., 1140., 1142., 1144.,\n",
       "         1146., 1148., 1150.]]),\n",
       " 'C3': array([[ 793.,  795.,  797.,  799.,  801.,  803.,  805.,  807.,  809.,\n",
       "          811.,  813.,  815.],\n",
       "        [ 841.,  843.,  845.,  847.,  849.,  851.,  853.,  855.,  857.,\n",
       "          859.,  861.,  863.],\n",
       "        [ 889.,  891.,  893.,  895.,  897.,  899.,  901.,  903.,  905.,\n",
       "          907.,  909.,  911.],\n",
       "        [ 937.,  939.,  941.,  943.,  945.,  947.,  949.,  951.,  953.,\n",
       "          955.,  957.,  959.],\n",
       "        [ 985.,  987.,  989.,  991.,  993.,  995.,  997.,  999., 1001.,\n",
       "         1003., 1005., 1007.],\n",
       "        [1033., 1035., 1037., 1039., 1041., 1043., 1045., 1047., 1049.,\n",
       "         1051., 1053., 1055.],\n",
       "        [1081., 1083., 1085., 1087., 1089., 1091., 1093., 1095., 1097.,\n",
       "         1099., 1101., 1103.],\n",
       "        [1129., 1131., 1133., 1135., 1137., 1139., 1141., 1143., 1145.,\n",
       "         1147., 1149., 1151.]])}"
      ]
     },
     "execution_count": 139,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "plates96TS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 157,
   "metadata": {},
   "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>Strain ID</th>\n",
       "      <th>ts allele</th>\n",
       "      <th>ts on SC</th>\n",
       "      <th>Background</th>\n",
       "      <th>Description</th>\n",
       "      <th>Genotype Mata</th>\n",
       "      <th>Plate</th>\n",
       "      <th>Row</th>\n",
       "      <th>Column</th>\n",
       "      <th>ORF</th>\n",
       "      <th>Gene</th>\n",
       "      <th>Decription</th>\n",
       "      <th>TS allele</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>1A</td>\n",
       "      <td>A</td>\n",
       "      <td>1</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>0</td>\n",
       "      <td>Blank</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TSA198</td>\n",
       "      <td>sed5-1</td>\n",
       "      <td>Lethal at 26°C</td>\n",
       "      <td>BY4741</td>\n",
       "      <td>cis-Golgi t-SNARE syntaxin; required for vesic...</td>\n",
       "      <td>sed5-1::KanR;  his3^1 leu2^0 ura3^0 met15^0</td>\n",
       "      <td>1A</td>\n",
       "      <td>A</td>\n",
       "      <td>2</td>\n",
       "      <td>YFR028C</td>\n",
       "      <td>CDC14</td>\n",
       "      <td>Protein phosphatase required for mitotic exit;...</td>\n",
       "      <td>cdc14-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TSA927</td>\n",
       "      <td>cdc21-1</td>\n",
       "      <td>Lethal at 26°C</td>\n",
       "      <td>BY4741</td>\n",
       "      <td>Thymidylate synthase; required for de novo bio...</td>\n",
       "      <td>cdc21-1::KanR;  his3^1 leu2^0 ura3^0 met15^0</td>\n",
       "      <td>1A</td>\n",
       "      <td>A</td>\n",
       "      <td>3</td>\n",
       "      <td>YLR026C</td>\n",
       "      <td>SED5</td>\n",
       "      <td>cis-Golgi t-SNARE syntaxin; required for vesic...</td>\n",
       "      <td>sed5-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>TSA496</td>\n",
       "      <td>nup192-15</td>\n",
       "      <td>Lethal at 26°C</td>\n",
       "      <td>BY4741</td>\n",
       "      <td>Essential subunit of inner ring of nuclear por...</td>\n",
       "      <td>nup192-15::KanR;  his3^1 leu2^0 ura3^0 met15^0</td>\n",
       "      <td>1A</td>\n",
       "      <td>A</td>\n",
       "      <td>4</td>\n",
       "      <td>YDL207W</td>\n",
       "      <td>GLE1</td>\n",
       "      <td>Cytoplasmic nucleoporin required for polyadeny...</td>\n",
       "      <td>gle1-4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>TSA166</td>\n",
       "      <td>mps1-1</td>\n",
       "      <td>Lethal at 26°C ~ 30°C</td>\n",
       "      <td>BY4741</td>\n",
       "      <td>Dual-specificity kinase; autophosphorylation r...</td>\n",
       "      <td>mps1-1::KanR;  his3^1 leu2^0 ura3^0 met15^0</td>\n",
       "      <td>1A</td>\n",
       "      <td>A</td>\n",
       "      <td>5</td>\n",
       "      <td>YOR074C</td>\n",
       "      <td>CDC21</td>\n",
       "      <td>Thymidylate synthase; required for de novo bio...</td>\n",
       "      <td>cdc21-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1144</th>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>3D</td>\n",
       "      <td>H</td>\n",
       "      <td>5</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1145</th>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>3D</td>\n",
       "      <td>H</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1146</th>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>3D</td>\n",
       "      <td>H</td>\n",
       "      <td>7</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1147</th>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>3D</td>\n",
       "      <td>H</td>\n",
       "      <td>8</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1148</th>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>nan</td>\n",
       "      <td>3D</td>\n",
       "      <td>H</td>\n",
       "      <td>9</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1149 rows × 13 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     Strain ID  ts allele               ts on SC Background  \\\n",
       "0        Blank      Blank                    nan        nan   \n",
       "1       TSA198     sed5-1         Lethal at 26°C     BY4741   \n",
       "2       TSA927    cdc21-1         Lethal at 26°C     BY4741   \n",
       "3       TSA496  nup192-15         Lethal at 26°C     BY4741   \n",
       "4       TSA166     mps1-1  Lethal at 26°C ~ 30°C     BY4741   \n",
       "...        ...        ...                    ...        ...   \n",
       "1144       nan        nan                    nan        nan   \n",
       "1145       nan        nan                    nan        nan   \n",
       "1146       nan        nan                    nan        nan   \n",
       "1147       nan        nan                    nan        nan   \n",
       "1148       nan        nan                    nan        nan   \n",
       "\n",
       "                                            Description  \\\n",
       "0                                                   nan   \n",
       "1     cis-Golgi t-SNARE syntaxin; required for vesic...   \n",
       "2     Thymidylate synthase; required for de novo bio...   \n",
       "3     Essential subunit of inner ring of nuclear por...   \n",
       "4     Dual-specificity kinase; autophosphorylation r...   \n",
       "...                                                 ...   \n",
       "1144                                                nan   \n",
       "1145                                                nan   \n",
       "1146                                                nan   \n",
       "1147                                                nan   \n",
       "1148                                                nan   \n",
       "\n",
       "                                       Genotype Mata Plate Row Column  \\\n",
       "0                                                nan    1A   A      1   \n",
       "1        sed5-1::KanR;  his3^1 leu2^0 ura3^0 met15^0    1A   A      2   \n",
       "2       cdc21-1::KanR;  his3^1 leu2^0 ura3^0 met15^0    1A   A      3   \n",
       "3     nup192-15::KanR;  his3^1 leu2^0 ura3^0 met15^0    1A   A      4   \n",
       "4        mps1-1::KanR;  his3^1 leu2^0 ura3^0 met15^0    1A   A      5   \n",
       "...                                              ...   ...  ..    ...   \n",
       "1144                                             nan    3D   H      5   \n",
       "1145                                             nan    3D   H      6   \n",
       "1146                                             nan    3D   H      7   \n",
       "1147                                             nan    3D   H      8   \n",
       "1148                                             nan    3D   H      9   \n",
       "\n",
       "          ORF   Gene                                         Decription  \\\n",
       "0       Blank  Blank                                                  0   \n",
       "1     YFR028C  CDC14  Protein phosphatase required for mitotic exit;...   \n",
       "2     YLR026C   SED5  cis-Golgi t-SNARE syntaxin; required for vesic...   \n",
       "3     YDL207W   GLE1  Cytoplasmic nucleoporin required for polyadeny...   \n",
       "4     YOR074C  CDC21  Thymidylate synthase; required for de novo bio...   \n",
       "...       ...    ...                                                ...   \n",
       "1144        0      0                                                  0   \n",
       "1145        0      0                                                  0   \n",
       "1146        0      0                                                  0   \n",
       "1147        0      0                                                  0   \n",
       "1148        0      0                                                  0   \n",
       "\n",
       "     TS allele  \n",
       "0        Blank  \n",
       "1      cdc14-3  \n",
       "2       sed5-1  \n",
       "3       gle1-4  \n",
       "4      cdc21-1  \n",
       "...        ...  \n",
       "1144         0  \n",
       "1145         0  \n",
       "1146         0  \n",
       "1147         0  \n",
       "1148         0  \n",
       "\n",
       "[1149 rows x 13 columns]"
      ]
     },
     "execution_count": 157,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Data96TS=[]\n",
    "i=0\n",
    "for P in range(1,3+1):\n",
    "    for L in ['A','B','C','D']:\n",
    "        for row in range(1,9):\n",
    "            for col in range(1,13):\n",
    "                i=int(plates96TS[L+str(P)][row-1][col-1])\n",
    "                new_line= []\n",
    "                [new_line.append(cell) for cell in list(TS_384.iloc[i].values[0:6])]\n",
    "                [new_line.append(cell) for cell in [str(P)+L,number[row], col]]\n",
    "                [new_line.append(cell) for cell in list(TS_384.iloc[i].values[9:])]\n",
    "                #print(new_line)\n",
    "                Data96TS.append(new_line)\n",
    "\n",
    "        \n",
    "Data96TS=np.vstack(Data96TS)\n",
    "\n",
    "Data96TS=pd.DataFrame(Data96TS, columns = list(TS_384.columns))\n",
    "\n",
    "Data96TS.head(-3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 198,
   "metadata": {},
   "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>Strain ID</th>\n",
       "      <th>ts allele</th>\n",
       "      <th>ts on SC</th>\n",
       "      <th>Background</th>\n",
       "      <th>Description</th>\n",
       "      <th>Genotype Mata</th>\n",
       "      <th>Plate</th>\n",
       "      <th>Row</th>\n",
       "      <th>Column</th>\n",
       "      <th>ORF</th>\n",
       "      <th>Gene</th>\n",
       "      <th>Decription</th>\n",
       "      <th>TS allele</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>1</td>\n",
       "      <td>Blank</td>\n",
       "      <td>Blank</td>\n",
       "      <td>0</td>\n",
       "      <td>Blank</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TSA146</td>\n",
       "      <td>cdc14-3</td>\n",
       "      <td>Lethal at 26°C</td>\n",
       "      <td>BY4741</td>\n",
       "      <td>Protein phosphatase required for mitotic exit;...</td>\n",
       "      <td>cdc14-3::KanR;  his3^1 leu2^0 ura3^0 met15^0</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>2</td>\n",
       "      <td>YOR046C</td>\n",
       "      <td>DBP5</td>\n",
       "      <td>Cytoplasmic ATP-dependent RNA helicase of the ...</td>\n",
       "      <td>dbp5-2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  Strain ID ts allele        ts on SC Background  \\\n",
       "0     Blank     Blank             NaN        NaN   \n",
       "1    TSA146   cdc14-3  Lethal at 26°C     BY4741   \n",
       "\n",
       "                                         Description  \\\n",
       "0                                                NaN   \n",
       "1  Protein phosphatase required for mitotic exit;...   \n",
       "\n",
       "                                  Genotype Mata  Plate Row  Column      ORF  \\\n",
       "0                                           NaN      1   A       1    Blank   \n",
       "1  cdc14-3::KanR;  his3^1 leu2^0 ura3^0 met15^0      1   A       2  YOR046C   \n",
       "\n",
       "    Gene                                         Decription TS allele  \n",
       "0  Blank                                                  0     Blank  \n",
       "1   DBP5  Cytoplasmic ATP-dependent RNA helicase of the ...    dbp5-2  "
      ]
     },
     "execution_count": 198,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "TS_384.head(2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 200,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([ True,  True,  True,  True,  True,  True,  True,  True,  True,\n",
       "        True,  True,  True,  True])"
      ]
     },
     "execution_count": 200,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "TS_384.columns == Data96TS.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 196,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Gene      ERG10\n",
      "Plate         1\n",
      "Row           B\n",
      "Column        1\n",
      "Name: 24, dtype: object\n",
      "      Gene Plate Row Column\n",
      "288  ERG10    1D   A      1\n"
     ]
    }
   ],
   "source": [
    "i=24\n",
    "print(TS_384[['Gene','Plate', 'Row','Column']].iloc[i])\n",
    "gene=TS_384['Strain ID'].iloc[i]\n",
    "new_i=np.where(Data96TS['Strain ID']==gene)[0]\n",
    "print(Data96TS[['Gene','Plate', 'Row','Column']].iloc[new_i])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 208,
   "metadata": {},
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "'str' object has no attribute 'append'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-208-2a36617286ec>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;34m[\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Files contain:\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mname\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mData96TS\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcolumns\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m<ipython-input-208-2a36617286ec>\u001b[0m in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;34m[\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Files contain:\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mname\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mData96TS\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcolumns\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m: 'str' object has no attribute 'append'"
     ]
    }
   ],
   "source": [
    "[(\"Files contain:\").append( name) for name in list(Data96TS.columns) ]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 221,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Temperature Sensitive (TS) Library\n",
      "\n",
      "\n",
      "For Details refer to Li et al. 2011 ( doi:10.1038/nbt.1832 )\n",
      "\n",
      "Gene Emplacement in:\n",
      " TS_Format96.csv and TS_Format384.csv (tab delimited) \n",
      "Files contains: Strain ID, ts allele, ts on SC, Background, Description, Genotype Mata, Plate, Row, Column, ORF, Gene, Decription, TS allele\n",
      "Replication Procedure:\n",
      "The YKO library was replicated in May 2021 by Paul Cachera (paucac@biosustain.dtu.dk) The libary in 384 arrays on agar (provided by Michael Lisby mlisby@bio.ku.dk) was transferred (Singers Rotor) to 96well plates filled with 120microL YPD (Flowrobotics Flowbot1). The plates were incubated @20C for approx 24h. 80uL of 50% glycerol was added to each well. Each well was mannually stirred with sterile Rotor pin pads\n"
     ]
    }
   ],
   "source": [
    "#save as csv tables\n",
    "Data96TS.to_csv(table_path+'TS_Format96.csv', sep='\\t')\n",
    "TS_384.to_csv(table_path+'TS_Format384.csv', sep='\\t')\n",
    "\n",
    "#write a read_me file:\n",
    "read_me = open(table_path+'Read_Me_TS.txt', 'w')\n",
    "corpus= 'Temperature Sensitive (TS) Library\\n\\n\\n'\n",
    "corpus+='For Details refer to Li et al. 2011 ( doi:10.1038/nbt.1832 )\\n\\n'\n",
    "corpus+='Gene Emplacement in:\\n TS_Format96.csv and TS_Format384.csv (tab delimited) \\n'\n",
    "#name columns in fils\n",
    "cols = []\n",
    "[cols.append(name+', ') for name in list(Data96TS.columns) ]\n",
    "cols = ''.join(cols)\n",
    "corpus+=\"Files contains: \" + cols[:-2] +'\\n'\n",
    "corpus+= 'Replication Procedure:\\n'\n",
    "corpus+='The YKO library was replicated in May 2021 by Paul Cachera (paucac@biosustain.dtu.dk) ' \n",
    "corpus+='The libary in 384 arrays on agar (provided by Michael Lisby mlisby@bio.ku.dk) was transferred (Singers Rotor) '\n",
    "corpus+='to 96well plates filled with 120microL YPD (Flowrobotics Flowbot1). The plates were incubated @20C for approx 24h. '\n",
    "corpus+='80uL of 50% glycerol was added to each well. Each well was mannually stirred with sterile Rotor pin pads'\n",
    "read_me.write(corpus)\n",
    "read_me.close()\n",
    "print(corpus)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 118,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "DNAEnv",
   "language": "python",
   "name": "dnaenv"
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  "language_info": {
   "codemirror_mode": {
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