P1 Helsinki combination.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from glob import glob\n",
    "import pandas as pd\n",
    "import re\n",
    "import matplotlib as mpl\n",
    "mpl.rcParams['pdf.fonttype'] = 42\n",
    "mpl.rcParams['ps.fonttype'] = 42"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# rename patient names in a txt\n",
    "def re_col_names(RNA_set):\n",
    "    '''rename patient names in a txt '''\n",
    "    Patient_name = [re.findall('(?<=star_Gencode.v39/).+(?=/)',  i) for i in RNA_set.columns.tolist()[6:]]\n",
    "    Patient_name = sum(Patient_name, [])\n",
    "    New_colnames = ['Geneid', 'Chr', 'Start', 'End', 'Strand', 'Length'] + Patient_name \n",
    "    RNA_set.columns = New_colnames\n",
    "    return RNA_set\n",
    "\n",
    "# get patient code list \n",
    "def get_patient_code(RNA_set):\n",
    "    '''get patient names in a txt '''\n",
    "    Patient_name = RNA_set.columns.tolist()[6:]\n",
    "    return Patient_name"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Helsinki"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Import data \n",
    "- All expression data were annotated with gencode.v39.primary_assembly.annotation.gtf as the reference"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Geneid</th>\n",
       "      <th>Chr</th>\n",
       "      <th>Start</th>\n",
       "      <th>End</th>\n",
       "      <th>Strand</th>\n",
       "      <th>Length</th>\n",
       "      <th>FM1338</th>\n",
       "      <th>FM2086</th>\n",
       "      <th>FM2440</th>\n",
       "      <th>FM2532</th>\n",
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       "      <th>FM3800</th>\n",
       "      <th>FM3814</th>\n",
       "      <th>FM3835</th>\n",
       "      <th>HL_VL_AMP08</th>\n",
       "      <th>JE_VL_AMP05</th>\n",
       "      <th>KO_AMP09</th>\n",
       "    </tr>\n",
       "  </thead>\n",
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       "      <th>0</th>\n",
       "      <td>ENSG00000223972.5</td>\n",
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       "      <td>449.0</td>\n",
       "      <td>207.0</td>\n",
       "      <td>695.0</td>\n",
       "      <td>572.0</td>\n",
       "      <td>881.0</td>\n",
       "      <td>708.0</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000278267.1</td>\n",
       "      <td>chr1</td>\n",
       "      <td>17369</td>\n",
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       "      <td>-</td>\n",
       "      <td>68.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>41.0</td>\n",
       "      <td>71.0</td>\n",
       "      <td>...</td>\n",
       "      <td>19.0</td>\n",
       "      <td>15.0</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000243485.5</td>\n",
       "      <td>chr1;chr1;chr1;chr1;chr1</td>\n",
       "      <td>29554;30267;30564;30976;30976</td>\n",
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       "<p>61589 rows × 26 columns</p>\n",
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      ],
      "text/plain": [
       "                  Geneid                                                Chr  \\\n",
       "0      ENSG00000223972.5       chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1   \n",
       "1      ENSG00000227232.5  chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;c...   \n",
       "2      ENSG00000278267.1                                               chr1   \n",
       "3      ENSG00000243485.5                           chr1;chr1;chr1;chr1;chr1   \n",
       "4      ENSG00000284332.1                                               chr1   \n",
       "...                  ...                                                ...   \n",
       "61584  ENSG00000276017.1                                         KI270734.1   \n",
       "61585  ENSG00000278817.1  KI270734.1;KI270734.1;KI270734.1;KI270734.1;KI...   \n",
       "61586  ENSG00000277196.4  KI270734.1;KI270734.1;KI270734.1;KI270734.1;KI...   \n",
       "61587  ENSG00000278625.1                                         KI270744.1   \n",
       "61588  ENSG00000277374.1                                         KI270750.1   \n",
       "\n",
       "                                                   Start  \\\n",
       "0      11869;12010;12179;12613;12613;12975;13221;1322...   \n",
       "1      14404;15005;15796;16607;16858;17233;17606;1791...   \n",
       "2                                                  17369   \n",
       "3                          29554;30267;30564;30976;30976   \n",
       "4                                                  30366   \n",
       "...                                                  ...   \n",
       "61584                                              72411   \n",
       "61585                 131494;131836;135443;136159;136845   \n",
       "61586  138082;138082;138743;138743;142194;142194;1436...   \n",
       "61587                                              51009   \n",
       "61588                                             148668   \n",
       "\n",
       "                                                     End  \\\n",
       "0      12227;12057;12227;12721;12697;13052;14409;1337...   \n",
       "1      14501;15038;15947;16765;17055;17368;17742;1806...   \n",
       "2                                                  17436   \n",
       "3                          30039;30667;30667;31109;31097   \n",
       "4                                                  30503   \n",
       "...                                                  ...   \n",
       "61584                                              74814   \n",
       "61585                 131755;131996;135543;136299;137392   \n",
       "61586  138667;138667;138831;138831;142292;142292;1437...   \n",
       "61587                                              51114   \n",
       "61588                                             148843   \n",
       "\n",
       "                                                  Strand  Length  FM1338  \\\n",
       "0                                      +;+;+;+;+;+;+;+;+  1735.0     2.0   \n",
       "1                                  -;-;-;-;-;-;-;-;-;-;-  1351.0   412.0   \n",
       "2                                                      -    68.0    36.0   \n",
       "3                                              +;+;+;+;+  1021.0     3.0   \n",
       "4                                                      +   138.0     0.0   \n",
       "...                                                  ...     ...     ...   \n",
       "61584                                                  +  2404.0     0.0   \n",
       "61585                                          +;+;+;+;+  1213.0  1043.0   \n",
       "61586  -;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;...  2405.0   311.0   \n",
       "61587                                                  -   106.0     0.0   \n",
       "61588                                                  +   176.0     0.0   \n",
       "\n",
       "       FM2086  FM2440  FM2532  ...  FM3690_2  FM3764  FM3796  FM3799  FM3800  \\\n",
       "0         2.0     1.0     1.0  ...       0.0     1.0     8.0     1.0     0.0   \n",
       "1       370.0   417.0   711.0  ...     207.0   281.0   454.0   263.0   449.0   \n",
       "2        15.0    41.0    71.0  ...      19.0    15.0    55.0     6.0    52.0   \n",
       "3         0.0     0.0     1.0  ...       0.0     0.0     1.0     3.0     1.0   \n",
       "4         0.0     0.0     0.0  ...       0.0     0.0     0.0     0.0     0.0   \n",
       "...       ...     ...     ...  ...       ...     ...     ...     ...     ...   \n",
       "61584     0.0     0.0     0.0  ...       0.0     0.0     0.0     0.0     0.0   \n",
       "61585  1151.0   282.0  1116.0  ...     747.0   876.0   592.0   479.0   250.0   \n",
       "61586   719.0    49.0   876.0  ...     147.0   240.0   415.0    48.0   405.0   \n",
       "61587     0.0     0.0     0.0  ...       0.0     0.0     0.0     0.0     0.0   \n",
       "61588     0.0     0.0     0.0  ...       0.0     0.0     0.0     0.0     0.0   \n",
       "\n",
       "       FM3814  FM3835  HL_VL_AMP08  JE_VL_AMP05  KO_AMP09  \n",
       "0         1.0     0.0          0.0          0.0       0.0  \n",
       "1       207.0   695.0        572.0        881.0     708.0  \n",
       "2        25.0    53.0         40.0         56.0      34.0  \n",
       "3         0.0     1.0          0.0          0.0       0.0  \n",
       "4         0.0     0.0          0.0          0.0       0.0  \n",
       "...       ...     ...          ...          ...       ...  \n",
       "61584     0.0     0.0          0.0          0.0       0.0  \n",
       "61585   405.0   892.0        617.0        927.0     687.0  \n",
       "61586   150.0   305.0       1023.0        429.0    2899.0  \n",
       "61587     0.0     0.0          0.0          0.0       0.0  \n",
       "61588     0.0     0.0          0.0          0.0       0.0  \n",
       "\n",
       "[61589 rows x 26 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Oxford0_poly = re_col_names(pd.read_csv('./Helsinki data/novogene_may2022_polyA_PE_samples_fragmentcounts_primary.txt', sep=\"\t\"))\n",
    "Oxford13_poly = re_col_names(pd.read_csv('./Helsinki data/oxford1_oxford3_polyA_PE_samples_fragmentcounts_primary.txt', sep=\"\t\"))\n",
    "Oxford4_ribo = re_col_names(pd.read_csv('./Helsinki data/oxford4_riboD_PE_samples_fragmentcounts_primary.txt', sep=\"\t\"))\n",
    "Oxford7_poly = re_col_names(pd.read_csv('./Helsinki data/oxford7_polyA_PE_samples_fragmentcounts_primary.txt', sep=\"\t\"))\n",
    "Oxford8_poly = re_col_names(pd.read_csv('./Helsinki data/oxford8_polyA_PE_samples_fragmentcounts_primary.txt', sep=\"\t\"))\n",
    "Oxford9_poly = re_col_names(pd.read_csv('./Helsinki data/oxford9_polyA_PE_samples_fragmentcounts_primary.txt', sep=\"\t\"))\n",
    "\n",
    "Oxford9_poly"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "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>Geneid</th>\n",
       "      <th>Chr</th>\n",
       "      <th>Start</th>\n",
       "      <th>End</th>\n",
       "      <th>Strand</th>\n",
       "      <th>Length</th>\n",
       "      <th>3804</th>\n",
       "      <th>4445</th>\n",
       "      <th>6172</th>\n",
       "      <th>AS_TA_AMP01</th>\n",
       "      <th>...</th>\n",
       "      <th>HL_VL_AMP08</th>\n",
       "      <th>IA_VL_AMP03</th>\n",
       "      <th>JE_VL_AMP05</th>\n",
       "      <th>JH</th>\n",
       "      <th>JH_VL_AMP04</th>\n",
       "      <th>KO_AMP09</th>\n",
       "      <th>MR_VL_AMP07</th>\n",
       "      <th>V-P_VL_AMP10</th>\n",
       "      <th>VA_VL_AMP06</th>\n",
       "      <th>VM_TA_AMP02</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000223972.5</td>\n",
       "      <td>chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1</td>\n",
       "      <td>11869;12010;12179;12613;12613;12975;13221;1322...</td>\n",
       "      <td>12227;12057;12227;12721;12697;13052;14409;1337...</td>\n",
       "      <td>+;+;+;+;+;+;+;+;+</td>\n",
       "      <td>1735</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000227232.5</td>\n",
       "      <td>chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;c...</td>\n",
       "      <td>14404;15005;15796;16607;16858;17233;17606;1791...</td>\n",
       "      <td>14501;15038;15947;16765;17055;17368;17742;1806...</td>\n",
       "      <td>-;-;-;-;-;-;-;-;-;-;-</td>\n",
       "      <td>1351</td>\n",
       "      <td>48</td>\n",
       "      <td>79</td>\n",
       "      <td>38</td>\n",
       "      <td>93</td>\n",
       "      <td>...</td>\n",
       "      <td>124</td>\n",
       "      <td>68</td>\n",
       "      <td>109</td>\n",
       "      <td>100</td>\n",
       "      <td>97</td>\n",
       "      <td>130</td>\n",
       "      <td>68</td>\n",
       "      <td>66</td>\n",
       "      <td>213</td>\n",
       "      <td>112</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000278267.1</td>\n",
       "      <td>chr1</td>\n",
       "      <td>17369</td>\n",
       "      <td>17436</td>\n",
       "      <td>-</td>\n",
       "      <td>68</td>\n",
       "      <td>11</td>\n",
       "      <td>5</td>\n",
       "      <td>6</td>\n",
       "      <td>4</td>\n",
       "      <td>...</td>\n",
       "      <td>28</td>\n",
       "      <td>11</td>\n",
       "      <td>17</td>\n",
       "      <td>6</td>\n",
       "      <td>19</td>\n",
       "      <td>10</td>\n",
       "      <td>5</td>\n",
       "      <td>8</td>\n",
       "      <td>12</td>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000243485.5</td>\n",
       "      <td>chr1;chr1;chr1;chr1;chr1</td>\n",
       "      <td>29554;30267;30564;30976;30976</td>\n",
       "      <td>30039;30667;30667;31109;31097</td>\n",
       "      <td>+;+;+;+;+</td>\n",
       "      <td>1021</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000284332.1</td>\n",
       "      <td>chr1</td>\n",
       "      <td>30366</td>\n",
       "      <td>30503</td>\n",
       "      <td>+</td>\n",
       "      <td>138</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</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",
       "      <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>61582</th>\n",
       "      <td>ENSG00000276017.1</td>\n",
       "      <td>KI270734.1</td>\n",
       "      <td>72411</td>\n",
       "      <td>74814</td>\n",
       "      <td>+</td>\n",
       "      <td>2404</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61583</th>\n",
       "      <td>ENSG00000278817.1</td>\n",
       "      <td>KI270734.1;KI270734.1;KI270734.1;KI270734.1;KI...</td>\n",
       "      <td>131494;131836;135443;136159;136845</td>\n",
       "      <td>131755;131996;135543;136299;137392</td>\n",
       "      <td>+;+;+;+;+</td>\n",
       "      <td>1213</td>\n",
       "      <td>308</td>\n",
       "      <td>168</td>\n",
       "      <td>434</td>\n",
       "      <td>1202</td>\n",
       "      <td>...</td>\n",
       "      <td>261</td>\n",
       "      <td>276</td>\n",
       "      <td>402</td>\n",
       "      <td>768</td>\n",
       "      <td>1023</td>\n",
       "      <td>382</td>\n",
       "      <td>215</td>\n",
       "      <td>404</td>\n",
       "      <td>145</td>\n",
       "      <td>315</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61584</th>\n",
       "      <td>ENSG00000277196.4</td>\n",
       "      <td>KI270734.1;KI270734.1;KI270734.1;KI270734.1;KI...</td>\n",
       "      <td>138082;138082;138743;138743;142194;142194;1436...</td>\n",
       "      <td>138667;138667;138831;138831;142292;142292;1437...</td>\n",
       "      <td>-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;...</td>\n",
       "      <td>2405</td>\n",
       "      <td>91</td>\n",
       "      <td>84</td>\n",
       "      <td>47</td>\n",
       "      <td>1432</td>\n",
       "      <td>...</td>\n",
       "      <td>514</td>\n",
       "      <td>187</td>\n",
       "      <td>189</td>\n",
       "      <td>3295</td>\n",
       "      <td>2598</td>\n",
       "      <td>1314</td>\n",
       "      <td>520</td>\n",
       "      <td>422</td>\n",
       "      <td>584</td>\n",
       "      <td>226</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61585</th>\n",
       "      <td>ENSG00000278625.1</td>\n",
       "      <td>KI270744.1</td>\n",
       "      <td>51009</td>\n",
       "      <td>51114</td>\n",
       "      <td>-</td>\n",
       "      <td>106</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61586</th>\n",
       "      <td>ENSG00000277374.1</td>\n",
       "      <td>KI270750.1</td>\n",
       "      <td>148668</td>\n",
       "      <td>148843</td>\n",
       "      <td>+</td>\n",
       "      <td>176</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</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>61587 rows × 60 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                  Geneid                                                Chr  \\\n",
       "0      ENSG00000223972.5       chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1   \n",
       "1      ENSG00000227232.5  chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;c...   \n",
       "2      ENSG00000278267.1                                               chr1   \n",
       "3      ENSG00000243485.5                           chr1;chr1;chr1;chr1;chr1   \n",
       "4      ENSG00000284332.1                                               chr1   \n",
       "...                  ...                                                ...   \n",
       "61582  ENSG00000276017.1                                         KI270734.1   \n",
       "61583  ENSG00000278817.1  KI270734.1;KI270734.1;KI270734.1;KI270734.1;KI...   \n",
       "61584  ENSG00000277196.4  KI270734.1;KI270734.1;KI270734.1;KI270734.1;KI...   \n",
       "61585  ENSG00000278625.1                                         KI270744.1   \n",
       "61586  ENSG00000277374.1                                         KI270750.1   \n",
       "\n",
       "                                                   Start  \\\n",
       "0      11869;12010;12179;12613;12613;12975;13221;1322...   \n",
       "1      14404;15005;15796;16607;16858;17233;17606;1791...   \n",
       "2                                                  17369   \n",
       "3                          29554;30267;30564;30976;30976   \n",
       "4                                                  30366   \n",
       "...                                                  ...   \n",
       "61582                                              72411   \n",
       "61583                 131494;131836;135443;136159;136845   \n",
       "61584  138082;138082;138743;138743;142194;142194;1436...   \n",
       "61585                                              51009   \n",
       "61586                                             148668   \n",
       "\n",
       "                                                     End  \\\n",
       "0      12227;12057;12227;12721;12697;13052;14409;1337...   \n",
       "1      14501;15038;15947;16765;17055;17368;17742;1806...   \n",
       "2                                                  17436   \n",
       "3                          30039;30667;30667;31109;31097   \n",
       "4                                                  30503   \n",
       "...                                                  ...   \n",
       "61582                                              74814   \n",
       "61583                 131755;131996;135543;136299;137392   \n",
       "61584  138667;138667;138831;138831;142292;142292;1437...   \n",
       "61585                                              51114   \n",
       "61586                                             148843   \n",
       "\n",
       "                                                  Strand  Length  3804  4445  \\\n",
       "0                                      +;+;+;+;+;+;+;+;+    1735     0     0   \n",
       "1                                  -;-;-;-;-;-;-;-;-;-;-    1351    48    79   \n",
       "2                                                      -      68    11     5   \n",
       "3                                              +;+;+;+;+    1021     0     0   \n",
       "4                                                      +     138     0     0   \n",
       "...                                                  ...     ...   ...   ...   \n",
       "61582                                                  +    2404     0     0   \n",
       "61583                                          +;+;+;+;+    1213   308   168   \n",
       "61584  -;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;...    2405    91    84   \n",
       "61585                                                  -     106     0     0   \n",
       "61586                                                  +     176     0     0   \n",
       "\n",
       "       6172  AS_TA_AMP01  ...  HL_VL_AMP08  IA_VL_AMP03  JE_VL_AMP05    JH  \\\n",
       "0         0            0  ...            0            0            0     1   \n",
       "1        38           93  ...          124           68          109   100   \n",
       "2         6            4  ...           28           11           17     6   \n",
       "3         0            0  ...            0            0            0     0   \n",
       "4         0            0  ...            0            0            0     0   \n",
       "...     ...          ...  ...          ...          ...          ...   ...   \n",
       "61582     0            0  ...            0            0            0     0   \n",
       "61583   434         1202  ...          261          276          402   768   \n",
       "61584    47         1432  ...          514          187          189  3295   \n",
       "61585     0            0  ...            0            0            0     0   \n",
       "61586     0            0  ...            0            0            0     0   \n",
       "\n",
       "       JH_VL_AMP04  KO_AMP09  MR_VL_AMP07  V-P_VL_AMP10  VA_VL_AMP06  \\\n",
       "0                0         0            0             0            0   \n",
       "1               97       130           68            66          213   \n",
       "2               19        10            5             8           12   \n",
       "3                0         0            0             0            0   \n",
       "4                0         0            0             0            0   \n",
       "...            ...       ...          ...           ...          ...   \n",
       "61582            0         0            0             0            0   \n",
       "61583         1023       382          215           404          145   \n",
       "61584         2598      1314          520           422          584   \n",
       "61585            0         0            0             0            0   \n",
       "61586            0         0            0             0            0   \n",
       "\n",
       "       VM_TA_AMP02  \n",
       "0                0  \n",
       "1              112  \n",
       "2               16  \n",
       "3                0  \n",
       "4                0  \n",
       "...            ...  \n",
       "61582            0  \n",
       "61583          315  \n",
       "61584          226  \n",
       "61585            0  \n",
       "61586            0  \n",
       "\n",
       "[61587 rows x 60 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Oxford13_poly"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Oxford0_poly_P: ['FM1812', 'FM22', 'FM2670', 'FM3310', 'FM3311', 'FM3591', 'FM3894', 'FM3901', 'FM4021', 'FM4024', 'FM4025', 'FM4028', 'FM4087', 'FM466', 'FM806', 'FM951', 'FM963', 'NEM_3613mbl', 'NEM_3613tubes', 'NEM_4743fbl', 'NEM_4743mbl', 'NEM_4743tubes', 'NEM_WTmbl', 'NEM_WTtubes']\n",
      "Oxford13_poly_P: ['3804', '4445', '6172', 'AS_TA_AMP01', 'FM1834', 'FM2259', 'FM2422', 'FM2428', 'FM2432', 'FM2433', 'FM2438', 'FM2511', 'FM2606', 'FM2616', 'FM2628', 'FM2633', 'FM2746', 'FM2864', 'FM2988', 'FM3017', 'FM3022', 'FM3060', 'FM3142', 'FM3206', 'FM3261', 'FM3262', 'FM3281', 'FM3288', 'FM3406', 'FM3407', 'FM3408', 'FM3409', 'FM3410', 'FM3411', 'FM3413', 'FM3415', 'FM3416', 'FM3417', 'FM3418', 'FM3421', 'FM3442', 'FM3459', 'FM846', 'FM957', 'HL_VL_AMP08', 'IA_VL_AMP03', 'JE_VL_AMP05', 'JH', 'JH_VL_AMP04', 'KO_AMP09', 'MR_VL_AMP07', 'V-P_VL_AMP10', 'VA_VL_AMP06', 'VM_TA_AMP02']\n",
      "Oxford4_ribo_P: ['3804', '4445', '6172', 'FM1834', 'FM2511', 'FM2616', 'FM3308', 'FM3206', 'FM3261', 'FM3262', 'FM3281', 'FM3288']\n",
      "Oxford7_poly_P: ['4974', '5930', '8061', 'FM2612', 'FM2621', 'FM2627', 'FM3198', 'FM3443', 'FM3479', 'FM3491', 'FM356', 'FM4220']\n",
      "Oxford8_poly_P: ['AS_TA_AMP01', 'FM1760', 'FM2251', 'FM2425', 'FM2481', 'FM2485', 'FM2763', 'FM2764', 'FM2827', 'FM3485', 'FM3597', 'FM3688', 'FM3689', 'FM3690', 'FM3692', 'HL_VL_AMP08', 'IA_VL_AMP03', 'JE_VL_AMP05', 'JH_VL_AMP04', 'KO_AMP09', 'MR_VL_AMP07', 'V-P_VL_AMP10', 'VA_VL_AMP06', 'VM_TA_AMP02']\n",
      "Oxford9_poly_P: ['FM1338', 'FM2086', 'FM2440', 'FM2532', 'FM2854', 'FM2861', 'FM3238', 'FM3257', 'FM3659', 'FM3690_1', 'FM3690_2', 'FM3764', 'FM3796', 'FM3799', 'FM3800', 'FM3814', 'FM3835', 'HL_VL_AMP08', 'JE_VL_AMP05', 'KO_AMP09']\n",
      "['AS_TA_AMP01', 'HL_VL_AMP08', 'IA_VL_AMP03', 'JE_VL_AMP05', 'JH_VL_AMP04', 'KO_AMP09', 'MR_VL_AMP07', 'V-P_VL_AMP10', 'VA_VL_AMP06', 'VM_TA_AMP02', 'HL_VL_AMP08', 'JE_VL_AMP05', 'KO_AMP09']\n"
     ]
    }
   ],
   "source": [
    "Oxford0_poly_P = get_patient_code(Oxford0_poly)\n",
    "print(f'Oxford0_poly_P: {Oxford0_poly_P}')\n",
    "\n",
    "Oxford13_poly_P = get_patient_code(Oxford13_poly)\n",
    "print(f'Oxford13_poly_P: {Oxford13_poly_P}')\n",
    "\n",
    "Oxford4_ribo_P = get_patient_code(Oxford4_ribo)\n",
    "print(f'Oxford4_ribo_P: {Oxford4_ribo_P}')\n",
    "\n",
    "Oxford7_poly_P = get_patient_code(Oxford7_poly)\n",
    "print(f'Oxford7_poly_P: {Oxford7_poly_P}')\n",
    "\n",
    "Oxford8_poly_P = get_patient_code(Oxford8_poly)\n",
    "print(f'Oxford8_poly_P: {Oxford8_poly_P}')\n",
    "\n",
    "Oxford9_poly_P = get_patient_code(Oxford9_poly)\n",
    "print(f'Oxford9_poly_P: {Oxford9_poly_P}')\n",
    "\n",
    "All_names = Oxford0_poly_P + Oxford13_poly_P +  Oxford7_poly_P + Oxford8_poly_P + Oxford9_poly_P\n",
    "\n",
    "# find duplicate \n",
    "\n",
    "Duplicate = [All_names[i] for i in range(len(All_names)) if not i == All_names.index(All_names[i])]\n",
    "print(Duplicate)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['AS_TA_AMP01',\n",
       " 'HL_VL_AMP08',\n",
       " 'IA_VL_AMP03',\n",
       " 'JE_VL_AMP05',\n",
       " 'JH_VL_AMP04',\n",
       " 'KO_AMP09',\n",
       " 'MR_VL_AMP07',\n",
       " 'V-P_VL_AMP10',\n",
       " 'VA_VL_AMP06',\n",
       " 'VM_TA_AMP02',\n",
       " 'HL_VL_AMP08',\n",
       " 'JE_VL_AMP05',\n",
       " 'KO_AMP09']"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Duplicate"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Add batch number to sample name"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['9_FM1338',\n",
       " '9_FM2086',\n",
       " '9_FM2440',\n",
       " '9_FM2532',\n",
       " '9_FM2854',\n",
       " '9_FM2861',\n",
       " '9_FM3238',\n",
       " '9_FM3257',\n",
       " '9_FM3659',\n",
       " '9_FM3690_1',\n",
       " '9_FM3690_2',\n",
       " '9_FM3764',\n",
       " '9_FM3796',\n",
       " '9_FM3799',\n",
       " '9_FM3800',\n",
       " '9_FM3814',\n",
       " '9_FM3835',\n",
       " '9_HL_VL_AMP08',\n",
       " '9_JE_VL_AMP05',\n",
       " '9_KO_AMP09']"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# add str to every patient name\n",
    "\n",
    "def addstrto_code(RNA_set, str):\n",
    "    '''add str to every patient name '''\n",
    "    Patient_name = RNA_set.columns.tolist()[6:]\n",
    "    Patient_name = [str + x for x in Patient_name]\n",
    "    New_colnames = ['Geneid', 'Chr', 'Start', 'End', 'Strand', 'Length'] + Patient_name \n",
    "    RNA_set.columns = New_colnames\n",
    "    return RNA_set\n",
    "\n",
    "Oxford0_poly = addstrto_code(Oxford0_poly, '0_')\n",
    "Oxford13_poly = addstrto_code(Oxford13_poly, '13_')\n",
    "Oxford7_poly = addstrto_code(Oxford7_poly, '7_')\n",
    "Oxford8_poly = addstrto_code(Oxford8_poly, '8_')\n",
    "Oxford9_poly = addstrto_code(Oxford9_poly, '9_')\n",
    "\n",
    "Oxford9_poly.columns.tolist()[6:]"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Merge"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['Geneid',\n",
       " 'Chr',\n",
       " 'Start',\n",
       " 'End',\n",
       " 'Strand',\n",
       " 'Length',\n",
       " '0_FM1812',\n",
       " '0_FM22',\n",
       " '0_FM2670',\n",
       " '0_FM3310',\n",
       " '0_FM3311',\n",
       " '0_FM3591',\n",
       " '0_FM3894',\n",
       " '0_FM3901',\n",
       " '0_FM4021',\n",
       " '0_FM4024',\n",
       " '0_FM4025',\n",
       " '0_FM4028',\n",
       " '0_FM4087',\n",
       " '0_FM466',\n",
       " '0_FM806',\n",
       " '0_FM951',\n",
       " '0_FM963',\n",
       " '0_NEM_3613mbl',\n",
       " '0_NEM_3613tubes',\n",
       " '0_NEM_4743fbl',\n",
       " '0_NEM_4743mbl',\n",
       " '0_NEM_4743tubes',\n",
       " '0_NEM_WTmbl',\n",
       " '0_NEM_WTtubes',\n",
       " '13_3804',\n",
       " '13_4445',\n",
       " '13_6172',\n",
       " '13_AS_TA_AMP01',\n",
       " '13_FM1834',\n",
       " '13_FM2259',\n",
       " '13_FM2422',\n",
       " '13_FM2428',\n",
       " '13_FM2432',\n",
       " '13_FM2433',\n",
       " '13_FM2438',\n",
       " '13_FM2511',\n",
       " '13_FM2606',\n",
       " '13_FM2616',\n",
       " '13_FM2628',\n",
       " '13_FM2633',\n",
       " '13_FM2746',\n",
       " '13_FM2864',\n",
       " '13_FM2988',\n",
       " '13_FM3017',\n",
       " '13_FM3022',\n",
       " '13_FM3060',\n",
       " '13_FM3142',\n",
       " '13_FM3206',\n",
       " '13_FM3261',\n",
       " '13_FM3262',\n",
       " '13_FM3281',\n",
       " '13_FM3288',\n",
       " '13_FM3406',\n",
       " '13_FM3407',\n",
       " '13_FM3408',\n",
       " '13_FM3409',\n",
       " '13_FM3410',\n",
       " '13_FM3411',\n",
       " '13_FM3413',\n",
       " '13_FM3415',\n",
       " '13_FM3416',\n",
       " '13_FM3417',\n",
       " '13_FM3418',\n",
       " '13_FM3421',\n",
       " '13_FM3442',\n",
       " '13_FM3459',\n",
       " '13_FM846',\n",
       " '13_FM957',\n",
       " '13_HL_VL_AMP08',\n",
       " '13_IA_VL_AMP03',\n",
       " '13_JE_VL_AMP05',\n",
       " '13_JH',\n",
       " '13_JH_VL_AMP04',\n",
       " '13_KO_AMP09',\n",
       " '13_MR_VL_AMP07',\n",
       " '13_V-P_VL_AMP10',\n",
       " '13_VA_VL_AMP06',\n",
       " '13_VM_TA_AMP02',\n",
       " '7_4974',\n",
       " '7_5930',\n",
       " '7_8061',\n",
       " '7_FM2612',\n",
       " '7_FM2621',\n",
       " '7_FM2627',\n",
       " '7_FM3198',\n",
       " '7_FM3443',\n",
       " '7_FM3479',\n",
       " '7_FM3491',\n",
       " '7_FM356',\n",
       " '7_FM4220',\n",
       " '8_AS_TA_AMP01',\n",
       " '8_FM1760',\n",
       " '8_FM2251',\n",
       " '8_FM2425',\n",
       " '8_FM2481',\n",
       " '8_FM2485',\n",
       " '8_FM2763',\n",
       " '8_FM2764',\n",
       " '8_FM2827',\n",
       " '8_FM3485',\n",
       " '8_FM3597',\n",
       " '8_FM3688',\n",
       " '8_FM3689',\n",
       " '8_FM3690',\n",
       " '8_FM3692',\n",
       " '8_HL_VL_AMP08',\n",
       " '8_IA_VL_AMP03',\n",
       " '8_JE_VL_AMP05',\n",
       " '8_JH_VL_AMP04',\n",
       " '8_KO_AMP09',\n",
       " '8_MR_VL_AMP07',\n",
       " '8_V-P_VL_AMP10',\n",
       " '8_VA_VL_AMP06',\n",
       " '8_VM_TA_AMP02',\n",
       " '9_FM1338',\n",
       " '9_FM2086',\n",
       " '9_FM2440',\n",
       " '9_FM2532',\n",
       " '9_FM2854',\n",
       " '9_FM2861',\n",
       " '9_FM3238',\n",
       " '9_FM3257',\n",
       " '9_FM3659',\n",
       " '9_FM3690_1',\n",
       " '9_FM3690_2',\n",
       " '9_FM3764',\n",
       " '9_FM3796',\n",
       " '9_FM3799',\n",
       " '9_FM3800',\n",
       " '9_FM3814',\n",
       " '9_FM3835',\n",
       " '9_HL_VL_AMP08',\n",
       " '9_JE_VL_AMP05',\n",
       " '9_KO_AMP09']"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merge_L.columns.tolist()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "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>Geneid</th>\n",
       "      <th>Chr</th>\n",
       "      <th>Start</th>\n",
       "      <th>End</th>\n",
       "      <th>Strand</th>\n",
       "      <th>Length</th>\n",
       "      <th>0_FM1812</th>\n",
       "      <th>0_FM22</th>\n",
       "      <th>0_FM2670</th>\n",
       "      <th>0_FM3310</th>\n",
       "      <th>...</th>\n",
       "      <th>9_FM3690_2</th>\n",
       "      <th>9_FM3764</th>\n",
       "      <th>9_FM3796</th>\n",
       "      <th>9_FM3799</th>\n",
       "      <th>9_FM3800</th>\n",
       "      <th>9_FM3814</th>\n",
       "      <th>9_FM3835</th>\n",
       "      <th>9_HL_VL_AMP08</th>\n",
       "      <th>9_JE_VL_AMP05</th>\n",
       "      <th>9_KO_AMP09</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000223972.5</td>\n",
       "      <td>chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1</td>\n",
       "      <td>11869;12010;12179;12613;12613;12975;13221;1322...</td>\n",
       "      <td>12227;12057;12227;12721;12697;13052;14409;1337...</td>\n",
       "      <td>+;+;+;+;+;+;+;+;+</td>\n",
       "      <td>1735</td>\n",
       "      <td>1</td>\n",
       "      <td>12</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000227232.5</td>\n",
       "      <td>chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;c...</td>\n",
       "      <td>14404;15005;15796;16607;16858;17233;17606;1791...</td>\n",
       "      <td>14501;15038;15947;16765;17055;17368;17742;1806...</td>\n",
       "      <td>-;-;-;-;-;-;-;-;-;-;-</td>\n",
       "      <td>1351</td>\n",
       "      <td>122</td>\n",
       "      <td>229</td>\n",
       "      <td>139</td>\n",
       "      <td>74</td>\n",
       "      <td>...</td>\n",
       "      <td>207.0</td>\n",
       "      <td>281.0</td>\n",
       "      <td>454.0</td>\n",
       "      <td>263.0</td>\n",
       "      <td>449.0</td>\n",
       "      <td>207.0</td>\n",
       "      <td>695.0</td>\n",
       "      <td>572.0</td>\n",
       "      <td>881.0</td>\n",
       "      <td>708.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000278267.1</td>\n",
       "      <td>chr1</td>\n",
       "      <td>17369</td>\n",
       "      <td>17436</td>\n",
       "      <td>-</td>\n",
       "      <td>68</td>\n",
       "      <td>22</td>\n",
       "      <td>28</td>\n",
       "      <td>9</td>\n",
       "      <td>8</td>\n",
       "      <td>...</td>\n",
       "      <td>19.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>55.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>52.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>53.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>56.0</td>\n",
       "      <td>34.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000243485.5</td>\n",
       "      <td>chr1;chr1;chr1;chr1;chr1</td>\n",
       "      <td>29554;30267;30564;30976;30976</td>\n",
       "      <td>30039;30667;30667;31109;31097</td>\n",
       "      <td>+;+;+;+;+</td>\n",
       "      <td>1021</td>\n",
       "      <td>6</td>\n",
       "      <td>10</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000284332.1</td>\n",
       "      <td>chr1</td>\n",
       "      <td>30366</td>\n",
       "      <td>30503</td>\n",
       "      <td>+</td>\n",
       "      <td>138</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</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",
       "      <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>61582</th>\n",
       "      <td>ENSG00000276017.1</td>\n",
       "      <td>KI270734.1</td>\n",
       "      <td>72411</td>\n",
       "      <td>74814</td>\n",
       "      <td>+</td>\n",
       "      <td>2404</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61583</th>\n",
       "      <td>ENSG00000278817.1</td>\n",
       "      <td>KI270734.1;KI270734.1;KI270734.1;KI270734.1;KI...</td>\n",
       "      <td>131494;131836;135443;136159;136845</td>\n",
       "      <td>131755;131996;135543;136299;137392</td>\n",
       "      <td>+;+;+;+;+</td>\n",
       "      <td>1213</td>\n",
       "      <td>264</td>\n",
       "      <td>186</td>\n",
       "      <td>660</td>\n",
       "      <td>472</td>\n",
       "      <td>...</td>\n",
       "      <td>747.0</td>\n",
       "      <td>876.0</td>\n",
       "      <td>592.0</td>\n",
       "      <td>479.0</td>\n",
       "      <td>250.0</td>\n",
       "      <td>405.0</td>\n",
       "      <td>892.0</td>\n",
       "      <td>617.0</td>\n",
       "      <td>927.0</td>\n",
       "      <td>687.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61584</th>\n",
       "      <td>ENSG00000277196.4</td>\n",
       "      <td>KI270734.1;KI270734.1;KI270734.1;KI270734.1;KI...</td>\n",
       "      <td>138082;138082;138743;138743;142194;142194;1436...</td>\n",
       "      <td>138667;138667;138831;138831;142292;142292;1437...</td>\n",
       "      <td>-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;...</td>\n",
       "      <td>2405</td>\n",
       "      <td>106</td>\n",
       "      <td>59</td>\n",
       "      <td>107</td>\n",
       "      <td>261</td>\n",
       "      <td>...</td>\n",
       "      <td>147.0</td>\n",
       "      <td>240.0</td>\n",
       "      <td>415.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>405.0</td>\n",
       "      <td>150.0</td>\n",
       "      <td>305.0</td>\n",
       "      <td>1023.0</td>\n",
       "      <td>429.0</td>\n",
       "      <td>2899.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61585</th>\n",
       "      <td>ENSG00000278625.1</td>\n",
       "      <td>KI270744.1</td>\n",
       "      <td>51009</td>\n",
       "      <td>51114</td>\n",
       "      <td>-</td>\n",
       "      <td>106</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61586</th>\n",
       "      <td>ENSG00000277374.1</td>\n",
       "      <td>KI270750.1</td>\n",
       "      <td>148668</td>\n",
       "      <td>148843</td>\n",
       "      <td>+</td>\n",
       "      <td>176</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>61587 rows × 140 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                  Geneid                                                Chr  \\\n",
       "0      ENSG00000223972.5       chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1   \n",
       "1      ENSG00000227232.5  chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;c...   \n",
       "2      ENSG00000278267.1                                               chr1   \n",
       "3      ENSG00000243485.5                           chr1;chr1;chr1;chr1;chr1   \n",
       "4      ENSG00000284332.1                                               chr1   \n",
       "...                  ...                                                ...   \n",
       "61582  ENSG00000276017.1                                         KI270734.1   \n",
       "61583  ENSG00000278817.1  KI270734.1;KI270734.1;KI270734.1;KI270734.1;KI...   \n",
       "61584  ENSG00000277196.4  KI270734.1;KI270734.1;KI270734.1;KI270734.1;KI...   \n",
       "61585  ENSG00000278625.1                                         KI270744.1   \n",
       "61586  ENSG00000277374.1                                         KI270750.1   \n",
       "\n",
       "                                                   Start  \\\n",
       "0      11869;12010;12179;12613;12613;12975;13221;1322...   \n",
       "1      14404;15005;15796;16607;16858;17233;17606;1791...   \n",
       "2                                                  17369   \n",
       "3                          29554;30267;30564;30976;30976   \n",
       "4                                                  30366   \n",
       "...                                                  ...   \n",
       "61582                                              72411   \n",
       "61583                 131494;131836;135443;136159;136845   \n",
       "61584  138082;138082;138743;138743;142194;142194;1436...   \n",
       "61585                                              51009   \n",
       "61586                                             148668   \n",
       "\n",
       "                                                     End  \\\n",
       "0      12227;12057;12227;12721;12697;13052;14409;1337...   \n",
       "1      14501;15038;15947;16765;17055;17368;17742;1806...   \n",
       "2                                                  17436   \n",
       "3                          30039;30667;30667;31109;31097   \n",
       "4                                                  30503   \n",
       "...                                                  ...   \n",
       "61582                                              74814   \n",
       "61583                 131755;131996;135543;136299;137392   \n",
       "61584  138667;138667;138831;138831;142292;142292;1437...   \n",
       "61585                                              51114   \n",
       "61586                                             148843   \n",
       "\n",
       "                                                  Strand  Length  0_FM1812  \\\n",
       "0                                      +;+;+;+;+;+;+;+;+    1735         1   \n",
       "1                                  -;-;-;-;-;-;-;-;-;-;-    1351       122   \n",
       "2                                                      -      68        22   \n",
       "3                                              +;+;+;+;+    1021         6   \n",
       "4                                                      +     138         0   \n",
       "...                                                  ...     ...       ...   \n",
       "61582                                                  +    2404         0   \n",
       "61583                                          +;+;+;+;+    1213       264   \n",
       "61584  -;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;-;...    2405       106   \n",
       "61585                                                  -     106         0   \n",
       "61586                                                  +     176         0   \n",
       "\n",
       "       0_FM22  0_FM2670  0_FM3310  ...  9_FM3690_2  9_FM3764  9_FM3796  \\\n",
       "0          12         2         7  ...         0.0       1.0       8.0   \n",
       "1         229       139        74  ...       207.0     281.0     454.0   \n",
       "2          28         9         8  ...        19.0      15.0      55.0   \n",
       "3          10         6         2  ...         0.0       0.0       1.0   \n",
       "4           0         0         0  ...         0.0       0.0       0.0   \n",
       "...       ...       ...       ...  ...         ...       ...       ...   \n",
       "61582       0         0         0  ...         0.0       0.0       0.0   \n",
       "61583     186       660       472  ...       747.0     876.0     592.0   \n",
       "61584      59       107       261  ...       147.0     240.0     415.0   \n",
       "61585       0         0         0  ...         0.0       0.0       0.0   \n",
       "61586       0         0         0  ...         0.0       0.0       0.0   \n",
       "\n",
       "       9_FM3799  9_FM3800  9_FM3814  9_FM3835  9_HL_VL_AMP08  9_JE_VL_AMP05  \\\n",
       "0           1.0       0.0       1.0       0.0            0.0            0.0   \n",
       "1         263.0     449.0     207.0     695.0          572.0          881.0   \n",
       "2           6.0      52.0      25.0      53.0           40.0           56.0   \n",
       "3           3.0       1.0       0.0       1.0            0.0            0.0   \n",
       "4           0.0       0.0       0.0       0.0            0.0            0.0   \n",
       "...         ...       ...       ...       ...            ...            ...   \n",
       "61582       0.0       0.0       0.0       0.0            0.0            0.0   \n",
       "61583     479.0     250.0     405.0     892.0          617.0          927.0   \n",
       "61584      48.0     405.0     150.0     305.0         1023.0          429.0   \n",
       "61585       0.0       0.0       0.0       0.0            0.0            0.0   \n",
       "61586       0.0       0.0       0.0       0.0            0.0            0.0   \n",
       "\n",
       "       9_KO_AMP09  \n",
       "0             0.0  \n",
       "1           708.0  \n",
       "2            34.0  \n",
       "3             0.0  \n",
       "4             0.0  \n",
       "...           ...  \n",
       "61582         0.0  \n",
       "61583       687.0  \n",
       "61584      2899.0  \n",
       "61585         0.0  \n",
       "61586         0.0  \n",
       "\n",
       "[61587 rows x 140 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merge_L = pd.merge(Oxford0_poly, Oxford13_poly.drop(Oxford13_poly.loc[:, 'Chr':'Length'].columns,axis = 1), how='left', on='Geneid')\n",
    "merge_L = pd.merge(merge_L, Oxford7_poly.drop(Oxford7_poly.loc[:, 'Chr':'Length'].columns,axis = 1), how='left', on='Geneid')\n",
    "merge_L = pd.merge(merge_L, Oxford8_poly.drop(Oxford8_poly.loc[:, 'Chr':'Length'].columns,axis = 1), how='left', on='Geneid')\n",
    "merge_L = pd.merge(merge_L, Oxford9_poly.drop(Oxford9_poly.loc[:, 'Chr':'Length'].columns,axis = 1), how='left', on='Geneid')\n",
    "merge_L"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "merge_L.drop(Oxford9_poly.loc[:, 'Chr':'Length'].columns,axis = 1).to_csv('Helsinki data/merge_L_Helsinki.csv', index=False)"
   ]
  }
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