geneseq_nlp_notebook.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# import necessary modules\n",
    "import pandas as pd\n",
    "pd.options.display.max_columns=1000\n",
    "pd.options.display.width=200\n",
    "pd.options.display.min_rows=60\n",
    "\n",
    "from sklearn import preprocessing \n",
    "from sklearn.feature_extraction.text import TfidfVectorizer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/gksullan/anaconda3/lib/python3.7/site-packages/IPython/core/interactiveshell.py:3058: DtypeWarning: Columns (34,36) have mixed types. Specify dtype option on import or set low_memory=False.\n",
      "  interactivity=interactivity, compiler=compiler, result=result)\n"
     ]
    },
    {
     "data": {
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       "<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>POS</th>\n",
       "      <th>REF</th>\n",
       "      <th>ALT</th>\n",
       "      <th>AF_ESP</th>\n",
       "      <th>AF_EXAC</th>\n",
       "      <th>AF_TGP</th>\n",
       "      <th>CLNDISDB</th>\n",
       "      <th>CLNDISDBINCL</th>\n",
       "      <th>CLNDN</th>\n",
       "      <th>CLNDNINCL</th>\n",
       "      <th>CLNHGVS</th>\n",
       "      <th>CLNSIGINCL</th>\n",
       "      <th>CLNVI</th>\n",
       "      <th>MC</th>\n",
       "      <th>ORIGIN</th>\n",
       "      <th>SSR</th>\n",
       "      <th>CLASS</th>\n",
       "      <th>Allele</th>\n",
       "      <th>Consequence</th>\n",
       "      <th>IMPACT</th>\n",
       "      <th>SYMBOL</th>\n",
       "      <th>Feature_type</th>\n",
       "      <th>Feature</th>\n",
       "      <th>EXON</th>\n",
       "      <th>INTRON</th>\n",
       "      <th>cDNA_position</th>\n",
       "      <th>CDS_position</th>\n",
       "      <th>Protein_position</th>\n",
       "      <th>Amino_acids</th>\n",
       "      <th>Codons</th>\n",
       "      <th>DISTANCE</th>\n",
       "      <th>STRAND</th>\n",
       "      <th>BAM_EDIT</th>\n",
       "      <th>PolyPhen</th>\n",
       "      <th>MOTIF_NAME</th>\n",
       "      <th>MOTIF_POS</th>\n",
       "      <th>HIGH_INF_POS</th>\n",
       "      <th>MOTIF_SCORE_CHANGE</th>\n",
       "      <th>LoFtool</th>\n",
       "      <th>CADD_PHRED</th>\n",
       "      <th>CADD_RAW</th>\n",
       "      <th>BLOSUM62</th>\n",
       "      <th>CHROM_1</th>\n",
       "      <th>CHROM_2</th>\n",
       "      <th>CHROM_3</th>\n",
       "      <th>CHROM_4</th>\n",
       "      <th>CHROM_5</th>\n",
       "      <th>CHROM_6</th>\n",
       "      <th>CHROM_7</th>\n",
       "      <th>CHROM_8</th>\n",
       "      <th>CHROM_9</th>\n",
       "      <th>CHROM_10</th>\n",
       "      <th>CHROM_11</th>\n",
       "      <th>CHROM_12</th>\n",
       "      <th>CHROM_13</th>\n",
       "      <th>CHROM_14</th>\n",
       "      <th>CHROM_15</th>\n",
       "      <th>CHROM_16</th>\n",
       "      <th>CHROM_16.1</th>\n",
       "      <th>CHROM_17</th>\n",
       "      <th>CHROM_18</th>\n",
       "      <th>CHROM_19</th>\n",
       "      <th>CHROM_20</th>\n",
       "      <th>CHROM_21</th>\n",
       "      <th>CHROM_22</th>\n",
       "      <th>CHROM_MT</th>\n",
       "      <th>CHROM_X</th>\n",
       "      <th>CLNVC_Deletion</th>\n",
       "      <th>CLNVC_Duplication</th>\n",
       "      <th>CLNVC_Indel</th>\n",
       "      <th>CLNVC_Insertion</th>\n",
       "      <th>CLNVC_Inversion</th>\n",
       "      <th>CLNVC_Microsatellite</th>\n",
       "      <th>CLNVC_single_nucleotide_variant</th>\n",
       "      <th>INT</th>\n",
       "      <th>EX</th>\n",
       "      <th>SIFT_deleterious</th>\n",
       "      <th>SIFT_deleterious_low_confidence</th>\n",
       "      <th>SIFT_tolerated</th>\n",
       "      <th>SIFT_tolerated_low_confidence</th>\n",
       "      <th>SIFT_unknown</th>\n",
       "      <th>BIOTYPE_misc_RNA</th>\n",
       "      <th>BIOTYPE_protein_coding</th>\n",
       "      <th>BIOTYPE_unknown</th>\n",
       "      <th>Length</th>\n",
       "      <th>Relative_Location</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>955563</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>MedGen:C3808739,OMIM:615120|MedGen:CN169374</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Myasthenic_syndrome,_congenital,_8|not_specified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NC_000001.10:g.955563G&gt;C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SO:0001583|missense_variant</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>C</td>\n",
       "      <td>missense_variant</td>\n",
       "      <td>MODERATE</td>\n",
       "      <td>AGRN</td>\n",
       "      <td>Transcript</td>\n",
       "      <td>NM_001305275.1</td>\n",
       "      <td>1/39</td>\n",
       "      <td>NaN</td>\n",
       "      <td>61</td>\n",
       "      <td>11</td>\n",
       "      <td>4.0</td>\n",
       "      <td>R/P</td>\n",
       "      <td>cGg/cCg</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\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>0.421</td>\n",
       "      <td>11.390</td>\n",
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       "      <td>2068.0</td>\n",
       "      <td>0.001934</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>955597</td>\n",
       "      <td>G</td>\n",
       "      <td>T</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.42418</td>\n",
       "      <td>0.2826</td>\n",
       "      <td>MedGen:CN169374</td>\n",
       "      <td>NaN</td>\n",
       "      <td>not_specified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NC_000001.10:g.955597G&gt;T</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SO:0001819|synonymous_variant</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>T</td>\n",
       "      <td>synonymous_variant</td>\n",
       "      <td>LOW</td>\n",
       "      <td>AGRN</td>\n",
       "      <td>Transcript</td>\n",
       "      <td>NM_001305275.1</td>\n",
       "      <td>1/39</td>\n",
       "      <td>NaN</td>\n",
       "      <td>95</td>\n",
       "      <td>45</td>\n",
       "      <td>15.0</td>\n",
       "      <td>P</td>\n",
       "      <td>ccG/ccT</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.421</td>\n",
       "      <td>8.150</td>\n",
       "      <td>0.599088</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1</td>\n",
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       "      <td>1</td>\n",
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       "      <td>1</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>2068.0</td>\n",
       "      <td>0.007253</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>955619</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.03475</td>\n",
       "      <td>0.0088</td>\n",
       "      <td>MedGen:C3808739,OMIM:615120|MedGen:CN169374</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Myasthenic_syndrome,_congenital,_8|not_specified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NC_000001.10:g.955619G&gt;C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SO:0001583|missense_variant</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1</td>\n",
       "      <td>C</td>\n",
       "      <td>missense_variant</td>\n",
       "      <td>MODERATE</td>\n",
       "      <td>AGRN</td>\n",
       "      <td>Transcript</td>\n",
       "      <td>NM_001305275.1</td>\n",
       "      <td>1/39</td>\n",
       "      <td>NaN</td>\n",
       "      <td>117</td>\n",
       "      <td>67</td>\n",
       "      <td>23.0</td>\n",
       "      <td>V/L</td>\n",
       "      <td>Gtc/Ctc</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\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>0.421</td>\n",
       "      <td>3.288</td>\n",
       "      <td>0.069819</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1</td>\n",
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       "      <td>2068.0</td>\n",
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>957640</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0.0318</td>\n",
       "      <td>0.02016</td>\n",
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       "      <td>MedGen:C3808739,OMIM:615120|MedGen:CN169374</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Myasthenic_syndrome,_congenital,_8|not_specified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NC_000001.10:g.957640C&gt;T</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SO:0001819|synonymous_variant</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
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       "      <td>synonymous_variant</td>\n",
       "      <td>LOW</td>\n",
       "      <td>AGRN</td>\n",
       "      <td>Transcript</td>\n",
       "      <td>NM_001305275.1</td>\n",
       "      <td>2/39</td>\n",
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       "      <td>261</td>\n",
       "      <td>87.0</td>\n",
       "      <td>D</td>\n",
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       "      <td>0.421</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>976059</td>\n",
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       "      <td>MedGen:CN169374</td>\n",
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       "      <td>NC_000001.10:g.976059C&gt;T</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SO:0001819|synonymous_variant</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1</td>\n",
       "      <td>T</td>\n",
       "      <td>synonymous_variant</td>\n",
       "      <td>LOW</td>\n",
       "      <td>AGRN</td>\n",
       "      <td>Transcript</td>\n",
       "      <td>NM_001305275.1</td>\n",
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       "      <td>576</td>\n",
       "      <td>526</td>\n",
       "      <td>176.0</td>\n",
       "      <td>L</td>\n",
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       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
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       "      <td>0.421</td>\n",
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       "      <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",
       "      <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",
       "      <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",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</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>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>2068.0</td>\n",
       "      <td>0.085106</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      POS REF ALT  AF_ESP  AF_EXAC  AF_TGP                                     CLNDISDB CLNDISDBINCL                                             CLNDN CLNDNINCL                   CLNHGVS CLNSIGINCL  \\\n",
       "0  955563   G   C  0.0000  0.00000  0.0000  MedGen:C3808739,OMIM:615120|MedGen:CN169374          NaN  Myasthenic_syndrome,_congenital,_8|not_specified       NaN  NC_000001.10:g.955563G>C        NaN   \n",
       "1  955597   G   T  0.0000  0.42418  0.2826                              MedGen:CN169374          NaN                                     not_specified       NaN  NC_000001.10:g.955597G>T        NaN   \n",
       "2  955619   G   C  0.0000  0.03475  0.0088  MedGen:C3808739,OMIM:615120|MedGen:CN169374          NaN  Myasthenic_syndrome,_congenital,_8|not_specified       NaN  NC_000001.10:g.955619G>C        NaN   \n",
       "3  957640   C   T  0.0318  0.02016  0.0328  MedGen:C3808739,OMIM:615120|MedGen:CN169374          NaN  Myasthenic_syndrome,_congenital,_8|not_specified       NaN  NC_000001.10:g.957640C>T        NaN   \n",
       "4  976059   C   T  0.0000  0.00022  0.0010                              MedGen:CN169374          NaN                                     not_specified       NaN  NC_000001.10:g.976059C>T        NaN   \n",
       "\n",
       "  CLNVI                             MC  ORIGIN  SSR  CLASS Allele         Consequence    IMPACT SYMBOL Feature_type         Feature  EXON INTRON cDNA_position CDS_position  Protein_position  \\\n",
       "0   NaN    SO:0001583|missense_variant     1.0  0.0      0      C    missense_variant  MODERATE   AGRN   Transcript  NM_001305275.1  1/39    NaN            61           11               4.0   \n",
       "1   NaN  SO:0001819|synonymous_variant     1.0  0.0      0      T  synonymous_variant       LOW   AGRN   Transcript  NM_001305275.1  1/39    NaN            95           45              15.0   \n",
       "2   NaN    SO:0001583|missense_variant     1.0  0.0      1      C    missense_variant  MODERATE   AGRN   Transcript  NM_001305275.1  1/39    NaN           117           67              23.0   \n",
       "3   NaN  SO:0001819|synonymous_variant     1.0  0.0      0      T  synonymous_variant       LOW   AGRN   Transcript  NM_001305275.1  2/39    NaN           311          261              87.0   \n",
       "4   NaN  SO:0001819|synonymous_variant     1.0  0.0      1      T  synonymous_variant       LOW   AGRN   Transcript  NM_001305275.1  4/39    NaN           576          526             176.0   \n",
       "\n",
       "  Amino_acids   Codons  DISTANCE  STRAND BAM_EDIT PolyPhen MOTIF_NAME  MOTIF_POS HIGH_INF_POS  MOTIF_SCORE_CHANGE  LoFtool  CADD_PHRED  CADD_RAW  BLOSUM62  CHROM_1  CHROM_2  CHROM_3  CHROM_4  \\\n",
       "0         R/P  cGg/cCg       NaN     1.0      NaN      NaN        NaN        NaN          NaN                 NaN    0.421      11.390  1.133255      -2.0        1        0        0        0   \n",
       "1           P  ccG/ccT       NaN     1.0      NaN      NaN        NaN        NaN          NaN                 NaN    0.421       8.150  0.599088       NaN        1        0        0        0   \n",
       "2         V/L  Gtc/Ctc       NaN     1.0      NaN      NaN        NaN        NaN          NaN                 NaN    0.421       3.288  0.069819       1.0        1        0        0        0   \n",
       "3           D  gaC/gaT       NaN     1.0      NaN      NaN        NaN        NaN          NaN                 NaN    0.421      12.560  1.356499       NaN        1        0        0        0   \n",
       "4           L  Ctg/Ttg       NaN     1.0      NaN      NaN        NaN        NaN          NaN                 NaN    0.421      17.740  2.234711       NaN        1        0        0        0   \n",
       "\n",
       "   CHROM_5  CHROM_6  CHROM_7  CHROM_8  CHROM_9  CHROM_10  CHROM_11  CHROM_12  CHROM_13  CHROM_14  CHROM_15  CHROM_16  CHROM_16.1  CHROM_17  CHROM_18  CHROM_19  CHROM_20  CHROM_21  CHROM_22  \\\n",
       "0        0        0        0        0        0         0         0         0         0         0         0         0           0         0         0         0         0         0         0   \n",
       "1        0        0        0        0        0         0         0         0         0         0         0         0           0         0         0         0         0         0         0   \n",
       "2        0        0        0        0        0         0         0         0         0         0         0         0           0         0         0         0         0         0         0   \n",
       "3        0        0        0        0        0         0         0         0         0         0         0         0           0         0         0         0         0         0         0   \n",
       "4        0        0        0        0        0         0         0         0         0         0         0         0           0         0         0         0         0         0         0   \n",
       "\n",
       "   CHROM_MT  CHROM_X  CLNVC_Deletion  CLNVC_Duplication  CLNVC_Indel  CLNVC_Insertion  CLNVC_Inversion  CLNVC_Microsatellite  CLNVC_single_nucleotide_variant  INT  EX  SIFT_deleterious  \\\n",
       "0         0        0               0                  0            0                0                0                     0                                1    0   1                 0   \n",
       "1         0        0               0                  0            0                0                0                     0                                1    0   1                 0   \n",
       "2         0        0               0                  0            0                0                0                     0                                1    0   1                 0   \n",
       "3         0        0               0                  0            0                0                0                     0                                1    0   1                 0   \n",
       "4         0        0               0                  0            0                0                0                     0                                1    0   1                 0   \n",
       "\n",
       "   SIFT_deleterious_low_confidence  SIFT_tolerated  SIFT_tolerated_low_confidence  SIFT_unknown  BIOTYPE_misc_RNA  BIOTYPE_protein_coding  BIOTYPE_unknown  Length  Relative_Location  \n",
       "0                                0               0                              0             1                 0                       1                0  2068.0           0.001934  \n",
       "1                                0               0                              0             1                 0                       1                0  2068.0           0.007253  \n",
       "2                                0               0                              0             1                 0                       1                0  2068.0           0.011122  \n",
       "3                                0               0                              0             1                 0                       1                0  2068.0           0.042070  \n",
       "4                                0               0                              0             1                 0                       1                0  2068.0           0.085106  "
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# read in cleaned data file\n",
    "df =  pd.read_csv('data/data_cleaned4.csv')\n",
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# create a TfidfVectorizer object, with tokenizer=list for the gene sequence strings\n",
    "vectorizer = TfidfVectorizer(tokenizer=list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['a', 'c', 'g', 't']\n",
      "(65188, 4)\n"
     ]
    }
   ],
   "source": [
    "# perform a .fit_transform on the \"REF\" column (reference allele)\n",
    "X_REF = vectorizer.fit_transform(df.REF)\n",
    "\n",
    "# print the feature names; should be the four nucleotide bases\n",
    "print(vectorizer.get_feature_names())\n",
    "\n",
    "# print the shape of the resultant csr sparse matrix\n",
    "print(X_REF.shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['a', 'c', 'g', 't']\n",
      "(65188, 4)\n"
     ]
    }
   ],
   "source": [
    "#perform the same steps as above on the \"ALT\" column, that is, the alternate allele\n",
    "X_ALT = vectorizer.fit_transform(df.ALT)\n",
    "print(vectorizer.get_feature_names())\n",
    "print(X_ALT.shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'sklearn.feature_extraction.text.TfidfVectorizer'>\n",
      "<class 'scipy.sparse.csr.csr_matrix'>\n"
     ]
    }
   ],
   "source": [
    "# dtype of vectorizer and X_ALT\n",
    "print(type(vectorizer))\n",
    "print(type(X_ALT))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "   ALT_a  ALT_c  ALT_g  ALT_t\n",
      "0    0.0    1.0    0.0    0.0\n",
      "1    0.0    0.0    0.0    1.0\n",
      "2    0.0    1.0    0.0    0.0\n",
      "3    0.0    0.0    0.0    1.0\n",
      "4    0.0    0.0    0.0    1.0\n",
      "   REF_a  REF_c  REF_g  REF_t\n",
      "0    0.0    0.0    1.0    0.0\n",
      "1    0.0    0.0    1.0    0.0\n",
      "2    0.0    0.0    1.0    0.0\n",
      "3    0.0    1.0    0.0    0.0\n",
      "4    0.0    1.0    0.0    0.0\n"
     ]
    }
   ],
   "source": [
    "# Convert the sparse matrix to a dense type, then use to create a data frame with \"ALT_\" & \"REF_\" column name prefixes\n",
    "tfidf_ALT = pd.DataFrame(X_ALT.todense(),columns=['ALT_' + x for x in vectorizer.get_feature_names()])\n",
    "tfidf_REF = pd.DataFrame(X_REF.todense(),columns=['REF_' + x for x in vectorizer.get_feature_names()])\n",
    "print(tfidf_ALT.head())\n",
    "print(tfidf_REF.head())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(65188, 4)\n",
      "(65188, 4)\n"
     ]
    }
   ],
   "source": [
    "print(tfidf_REF.shape)\n",
    "print(tfidf_ALT.shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "134"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Check an entry where there is more than one nucleotide represented (i.e. the sum across all four bases does not equal zero)\n",
    "list(tfidf_ALT.T.sum() > 1).index(True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "ALT_a    0.000000\n",
       "ALT_c    0.784158\n",
       "ALT_g    0.000000\n",
       "ALT_t    0.620561\n",
       "Name: 134, dtype: float64"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# View the ALT allele values in the sparse matrix \n",
    "tfidf_ALT.iloc[134]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "POS                                                                          2338230\n",
       "REF                                                                                C\n",
       "ALT                                                                               CT\n",
       "AF_ESP                                                                             0\n",
       "AF_EXAC                                                                            0\n",
       "AF_TGP                                                                             0\n",
       "CLNDISDB                           MedGen:C3553947,OMIM:614870|MedGen:C3553948,OM...\n",
       "CLNDISDBINCL                                                                     NaN\n",
       "CLNDN                              Peroxisome_biogenesis_disorder_6A|Peroxisome_b...\n",
       "CLNDNINCL                                                                        NaN\n",
       "CLNHGVS                                                   NC_000001.10:g.2338231dupT\n",
       "CLNSIGINCL                                                                       NaN\n",
       "CLNVI                                               OMIM_Allelic_Variant:602859.0005\n",
       "MC                                                     SO:0001589|frameshift_variant\n",
       "ORIGIN                                                                             1\n",
       "SSR                                                                                0\n",
       "CLASS                                                                              0\n",
       "Allele                                                                             T\n",
       "Consequence                                                       frameshift_variant\n",
       "IMPACT                                                                          HIGH\n",
       "SYMBOL                                                                         PEX10\n",
       "Feature_type                                                              Transcript\n",
       "Feature                                                                  NM_153818.1\n",
       "EXON                                                                             4/6\n",
       "INTRON                                                                           NaN\n",
       "cDNA_position                                                                833-834\n",
       "CDS_position                                                                 764-765\n",
       "Protein_position                                                                 255\n",
       "Amino_acids                                                                     Q/QX\n",
       "Codons                                                                      cag/caAg\n",
       "                                                         ...                        \n",
       "CHROM_15                                                                           0\n",
       "CHROM_16                                                                           0\n",
       "CHROM_16.1                                                                         0\n",
       "CHROM_17                                                                           0\n",
       "CHROM_18                                                                           0\n",
       "CHROM_19                                                                           0\n",
       "CHROM_20                                                                           0\n",
       "CHROM_21                                                                           0\n",
       "CHROM_22                                                                           0\n",
       "CHROM_MT                                                                           0\n",
       "CHROM_X                                                                            0\n",
       "CLNVC_Deletion                                                                     0\n",
       "CLNVC_Duplication                                                                  1\n",
       "CLNVC_Indel                                                                        0\n",
       "CLNVC_Insertion                                                                    0\n",
       "CLNVC_Inversion                                                                    0\n",
       "CLNVC_Microsatellite                                                               0\n",
       "CLNVC_single_nucleotide_variant                                                    0\n",
       "INT                                                                                0\n",
       "EX                                                                                 1\n",
       "SIFT_deleterious                                                                   0\n",
       "SIFT_deleterious_low_confidence                                                    0\n",
       "SIFT_tolerated                                                                     0\n",
       "SIFT_tolerated_low_confidence                                                      0\n",
       "SIFT_unknown                                                                       1\n",
       "BIOTYPE_misc_RNA                                                                   0\n",
       "BIOTYPE_protein_coding                                                             1\n",
       "BIOTYPE_unknown                                                                    0\n",
       "Length                                                                           326\n",
       "Relative_Location                                                           0.782209\n",
       "Name: 134, Length: 86, dtype: object"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Confirm the distribution created by TfidfVectorizer matches with the actual ALT allele = \"CT\" -- it does!\n",
    "df.iloc[134]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Concatenate the newly engineered 8 features (4 from REF and 4 from ALT into the original dataframe)\n",
    "df_nlp2 = pd.concat([df,tfidf_REF,tfidf_ALT], axis=1, sort=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "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>POS</th>\n",
       "      <th>REF</th>\n",
       "      <th>ALT</th>\n",
       "      <th>AF_ESP</th>\n",
       "      <th>AF_EXAC</th>\n",
       "      <th>AF_TGP</th>\n",
       "      <th>CLNDISDB</th>\n",
       "      <th>CLNDISDBINCL</th>\n",
       "      <th>CLNDN</th>\n",
       "      <th>CLNDNINCL</th>\n",
       "      <th>CLNHGVS</th>\n",
       "      <th>CLNSIGINCL</th>\n",
       "      <th>CLNVI</th>\n",
       "      <th>MC</th>\n",
       "      <th>ORIGIN</th>\n",
       "      <th>SSR</th>\n",
       "      <th>CLASS</th>\n",
       "      <th>Allele</th>\n",
       "      <th>Consequence</th>\n",
       "      <th>IMPACT</th>\n",
       "      <th>SYMBOL</th>\n",
       "      <th>Feature_type</th>\n",
       "      <th>Feature</th>\n",
       "      <th>EXON</th>\n",
       "      <th>INTRON</th>\n",
       "      <th>cDNA_position</th>\n",
       "      <th>CDS_position</th>\n",
       "      <th>Protein_position</th>\n",
       "      <th>Amino_acids</th>\n",
       "      <th>Codons</th>\n",
       "      <th>DISTANCE</th>\n",
       "      <th>STRAND</th>\n",
       "      <th>BAM_EDIT</th>\n",
       "      <th>PolyPhen</th>\n",
       "      <th>MOTIF_NAME</th>\n",
       "      <th>MOTIF_POS</th>\n",
       "      <th>HIGH_INF_POS</th>\n",
       "      <th>MOTIF_SCORE_CHANGE</th>\n",
       "      <th>LoFtool</th>\n",
       "      <th>CADD_PHRED</th>\n",
       "      <th>CADD_RAW</th>\n",
       "      <th>BLOSUM62</th>\n",
       "      <th>CHROM_1</th>\n",
       "      <th>CHROM_2</th>\n",
       "      <th>CHROM_3</th>\n",
       "      <th>CHROM_4</th>\n",
       "      <th>CHROM_5</th>\n",
       "      <th>CHROM_6</th>\n",
       "      <th>CHROM_7</th>\n",
       "      <th>CHROM_8</th>\n",
       "      <th>CHROM_9</th>\n",
       "      <th>CHROM_10</th>\n",
       "      <th>CHROM_11</th>\n",
       "      <th>CHROM_12</th>\n",
       "      <th>CHROM_13</th>\n",
       "      <th>CHROM_14</th>\n",
       "      <th>CHROM_15</th>\n",
       "      <th>CHROM_16</th>\n",
       "      <th>CHROM_16.1</th>\n",
       "      <th>CHROM_17</th>\n",
       "      <th>CHROM_18</th>\n",
       "      <th>CHROM_19</th>\n",
       "      <th>CHROM_20</th>\n",
       "      <th>CHROM_21</th>\n",
       "      <th>CHROM_22</th>\n",
       "      <th>CHROM_MT</th>\n",
       "      <th>CHROM_X</th>\n",
       "      <th>CLNVC_Deletion</th>\n",
       "      <th>CLNVC_Duplication</th>\n",
       "      <th>CLNVC_Indel</th>\n",
       "      <th>CLNVC_Insertion</th>\n",
       "      <th>CLNVC_Inversion</th>\n",
       "      <th>CLNVC_Microsatellite</th>\n",
       "      <th>CLNVC_single_nucleotide_variant</th>\n",
       "      <th>INT</th>\n",
       "      <th>EX</th>\n",
       "      <th>SIFT_deleterious</th>\n",
       "      <th>SIFT_deleterious_low_confidence</th>\n",
       "      <th>SIFT_tolerated</th>\n",
       "      <th>SIFT_tolerated_low_confidence</th>\n",
       "      <th>SIFT_unknown</th>\n",
       "      <th>BIOTYPE_misc_RNA</th>\n",
       "      <th>BIOTYPE_protein_coding</th>\n",
       "      <th>BIOTYPE_unknown</th>\n",
       "      <th>Length</th>\n",
       "      <th>Relative_Location</th>\n",
       "      <th>REF_a</th>\n",
       "      <th>REF_c</th>\n",
       "      <th>REF_g</th>\n",
       "      <th>REF_t</th>\n",
       "      <th>ALT_a</th>\n",
       "      <th>ALT_c</th>\n",
       "      <th>ALT_g</th>\n",
       "      <th>ALT_t</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>955563</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>MedGen:C3808739,OMIM:615120|MedGen:CN169374</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Myasthenic_syndrome,_congenital,_8|not_specified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NC_000001.10:g.955563G&gt;C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SO:0001583|missense_variant</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>C</td>\n",
       "      <td>missense_variant</td>\n",
       "      <td>MODERATE</td>\n",
       "      <td>AGRN</td>\n",
       "      <td>Transcript</td>\n",
       "      <td>NM_001305275.1</td>\n",
       "      <td>1/39</td>\n",
       "      <td>NaN</td>\n",
       "      <td>61</td>\n",
       "      <td>11</td>\n",
       "      <td>4.0</td>\n",
       "      <td>R/P</td>\n",
       "      <td>cGg/cCg</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\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>0.421</td>\n",
       "      <td>11.390</td>\n",
       "      <td>1.133255</td>\n",
       "      <td>-2.0</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",
       "      <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",
       "      <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",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</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>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>2068.0</td>\n",
       "      <td>0.001934</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>955597</td>\n",
       "      <td>G</td>\n",
       "      <td>T</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.42418</td>\n",
       "      <td>0.2826</td>\n",
       "      <td>MedGen:CN169374</td>\n",
       "      <td>NaN</td>\n",
       "      <td>not_specified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NC_000001.10:g.955597G&gt;T</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SO:0001819|synonymous_variant</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>T</td>\n",
       "      <td>synonymous_variant</td>\n",
       "      <td>LOW</td>\n",
       "      <td>AGRN</td>\n",
       "      <td>Transcript</td>\n",
       "      <td>NM_001305275.1</td>\n",
       "      <td>1/39</td>\n",
       "      <td>NaN</td>\n",
       "      <td>95</td>\n",
       "      <td>45</td>\n",
       "      <td>15.0</td>\n",
       "      <td>P</td>\n",
       "      <td>ccG/ccT</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\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>0.421</td>\n",
       "      <td>8.150</td>\n",
       "      <td>0.599088</td>\n",
       "      <td>NaN</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",
       "      <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",
       "      <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",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</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>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>2068.0</td>\n",
       "      <td>0.007253</td>\n",
       "      <td>0.0</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",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>955619</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.03475</td>\n",
       "      <td>0.0088</td>\n",
       "      <td>MedGen:C3808739,OMIM:615120|MedGen:CN169374</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Myasthenic_syndrome,_congenital,_8|not_specified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NC_000001.10:g.955619G&gt;C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SO:0001583|missense_variant</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1</td>\n",
       "      <td>C</td>\n",
       "      <td>missense_variant</td>\n",
       "      <td>MODERATE</td>\n",
       "      <td>AGRN</td>\n",
       "      <td>Transcript</td>\n",
       "      <td>NM_001305275.1</td>\n",
       "      <td>1/39</td>\n",
       "      <td>NaN</td>\n",
       "      <td>117</td>\n",
       "      <td>67</td>\n",
       "      <td>23.0</td>\n",
       "      <td>V/L</td>\n",
       "      <td>Gtc/Ctc</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\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>0.421</td>\n",
       "      <td>3.288</td>\n",
       "      <td>0.069819</td>\n",
       "      <td>1.0</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",
       "      <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",
       "      <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",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</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>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>2068.0</td>\n",
       "      <td>0.011122</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>957640</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0.0318</td>\n",
       "      <td>0.02016</td>\n",
       "      <td>0.0328</td>\n",
       "      <td>MedGen:C3808739,OMIM:615120|MedGen:CN169374</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Myasthenic_syndrome,_congenital,_8|not_specified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NC_000001.10:g.957640C&gt;T</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SO:0001819|synonymous_variant</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>T</td>\n",
       "      <td>synonymous_variant</td>\n",
       "      <td>LOW</td>\n",
       "      <td>AGRN</td>\n",
       "      <td>Transcript</td>\n",
       "      <td>NM_001305275.1</td>\n",
       "      <td>2/39</td>\n",
       "      <td>NaN</td>\n",
       "      <td>311</td>\n",
       "      <td>261</td>\n",
       "      <td>87.0</td>\n",
       "      <td>D</td>\n",
       "      <td>gaC/gaT</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\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>0.421</td>\n",
       "      <td>12.560</td>\n",
       "      <td>1.356499</td>\n",
       "      <td>NaN</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",
       "      <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",
       "      <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",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</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>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>2068.0</td>\n",
       "      <td>0.042070</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",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>976059</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.00022</td>\n",
       "      <td>0.0010</td>\n",
       "      <td>MedGen:CN169374</td>\n",
       "      <td>NaN</td>\n",
       "      <td>not_specified</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NC_000001.10:g.976059C&gt;T</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SO:0001819|synonymous_variant</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1</td>\n",
       "      <td>T</td>\n",
       "      <td>synonymous_variant</td>\n",
       "      <td>LOW</td>\n",
       "      <td>AGRN</td>\n",
       "      <td>Transcript</td>\n",
       "      <td>NM_001305275.1</td>\n",
       "      <td>4/39</td>\n",
       "      <td>NaN</td>\n",
       "      <td>576</td>\n",
       "      <td>526</td>\n",
       "      <td>176.0</td>\n",
       "      <td>L</td>\n",
       "      <td>Ctg/Ttg</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\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>0.421</td>\n",
       "      <td>17.740</td>\n",
       "      <td>2.234711</td>\n",
       "      <td>NaN</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",
       "      <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",
       "      <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",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</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>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>2068.0</td>\n",
       "      <td>0.085106</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",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      POS REF ALT  AF_ESP  AF_EXAC  AF_TGP                                     CLNDISDB CLNDISDBINCL                                             CLNDN CLNDNINCL                   CLNHGVS CLNSIGINCL  \\\n",
       "0  955563   G   C  0.0000  0.00000  0.0000  MedGen:C3808739,OMIM:615120|MedGen:CN169374          NaN  Myasthenic_syndrome,_congenital,_8|not_specified       NaN  NC_000001.10:g.955563G>C        NaN   \n",
       "1  955597   G   T  0.0000  0.42418  0.2826                              MedGen:CN169374          NaN                                     not_specified       NaN  NC_000001.10:g.955597G>T        NaN   \n",
       "2  955619   G   C  0.0000  0.03475  0.0088  MedGen:C3808739,OMIM:615120|MedGen:CN169374          NaN  Myasthenic_syndrome,_congenital,_8|not_specified       NaN  NC_000001.10:g.955619G>C        NaN   \n",
       "3  957640   C   T  0.0318  0.02016  0.0328  MedGen:C3808739,OMIM:615120|MedGen:CN169374          NaN  Myasthenic_syndrome,_congenital,_8|not_specified       NaN  NC_000001.10:g.957640C>T        NaN   \n",
       "4  976059   C   T  0.0000  0.00022  0.0010                              MedGen:CN169374          NaN                                     not_specified       NaN  NC_000001.10:g.976059C>T        NaN   \n",
       "\n",
       "  CLNVI                             MC  ORIGIN  SSR  CLASS Allele         Consequence    IMPACT SYMBOL Feature_type         Feature  EXON INTRON cDNA_position CDS_position  Protein_position  \\\n",
       "0   NaN    SO:0001583|missense_variant     1.0  0.0      0      C    missense_variant  MODERATE   AGRN   Transcript  NM_001305275.1  1/39    NaN            61           11               4.0   \n",
       "1   NaN  SO:0001819|synonymous_variant     1.0  0.0      0      T  synonymous_variant       LOW   AGRN   Transcript  NM_001305275.1  1/39    NaN            95           45              15.0   \n",
       "2   NaN    SO:0001583|missense_variant     1.0  0.0      1      C    missense_variant  MODERATE   AGRN   Transcript  NM_001305275.1  1/39    NaN           117           67              23.0   \n",
       "3   NaN  SO:0001819|synonymous_variant     1.0  0.0      0      T  synonymous_variant       LOW   AGRN   Transcript  NM_001305275.1  2/39    NaN           311          261              87.0   \n",
       "4   NaN  SO:0001819|synonymous_variant     1.0  0.0      1      T  synonymous_variant       LOW   AGRN   Transcript  NM_001305275.1  4/39    NaN           576          526             176.0   \n",
       "\n",
       "  Amino_acids   Codons  DISTANCE  STRAND BAM_EDIT PolyPhen MOTIF_NAME  MOTIF_POS HIGH_INF_POS  MOTIF_SCORE_CHANGE  LoFtool  CADD_PHRED  CADD_RAW  BLOSUM62  CHROM_1  CHROM_2  CHROM_3  CHROM_4  \\\n",
       "0         R/P  cGg/cCg       NaN     1.0      NaN      NaN        NaN        NaN          NaN                 NaN    0.421      11.390  1.133255      -2.0        1        0        0        0   \n",
       "1           P  ccG/ccT       NaN     1.0      NaN      NaN        NaN        NaN          NaN                 NaN    0.421       8.150  0.599088       NaN        1        0        0        0   \n",
       "2         V/L  Gtc/Ctc       NaN     1.0      NaN      NaN        NaN        NaN          NaN                 NaN    0.421       3.288  0.069819       1.0        1        0        0        0   \n",
       "3           D  gaC/gaT       NaN     1.0      NaN      NaN        NaN        NaN          NaN                 NaN    0.421      12.560  1.356499       NaN        1        0        0        0   \n",
       "4           L  Ctg/Ttg       NaN     1.0      NaN      NaN        NaN        NaN          NaN                 NaN    0.421      17.740  2.234711       NaN        1        0        0        0   \n",
       "\n",
       "   CHROM_5  CHROM_6  CHROM_7  CHROM_8  CHROM_9  CHROM_10  CHROM_11  CHROM_12  CHROM_13  CHROM_14  CHROM_15  CHROM_16  CHROM_16.1  CHROM_17  CHROM_18  CHROM_19  CHROM_20  CHROM_21  CHROM_22  \\\n",
       "0        0        0        0        0        0         0         0         0         0         0         0         0           0         0         0         0         0         0         0   \n",
       "1        0        0        0        0        0         0         0         0         0         0         0         0           0         0         0         0         0         0         0   \n",
       "2        0        0        0        0        0         0         0         0         0         0         0         0           0         0         0         0         0         0         0   \n",
       "3        0        0        0        0        0         0         0         0         0         0         0         0           0         0         0         0         0         0         0   \n",
       "4        0        0        0        0        0         0         0         0         0         0         0         0           0         0         0         0         0         0         0   \n",
       "\n",
       "   CHROM_MT  CHROM_X  CLNVC_Deletion  CLNVC_Duplication  CLNVC_Indel  CLNVC_Insertion  CLNVC_Inversion  CLNVC_Microsatellite  CLNVC_single_nucleotide_variant  INT  EX  SIFT_deleterious  \\\n",
       "0         0        0               0                  0            0                0                0                     0                                1    0   1                 0   \n",
       "1         0        0               0                  0            0                0                0                     0                                1    0   1                 0   \n",
       "2         0        0               0                  0            0                0                0                     0                                1    0   1                 0   \n",
       "3         0        0               0                  0            0                0                0                     0                                1    0   1                 0   \n",
       "4         0        0               0                  0            0                0                0                     0                                1    0   1                 0   \n",
       "\n",
       "   SIFT_deleterious_low_confidence  SIFT_tolerated  SIFT_tolerated_low_confidence  SIFT_unknown  BIOTYPE_misc_RNA  BIOTYPE_protein_coding  BIOTYPE_unknown  Length  Relative_Location  REF_a  REF_c  \\\n",
       "0                                0               0                              0             1                 0                       1                0  2068.0           0.001934    0.0    0.0   \n",
       "1                                0               0                              0             1                 0                       1                0  2068.0           0.007253    0.0    0.0   \n",
       "2                                0               0                              0             1                 0                       1                0  2068.0           0.011122    0.0    0.0   \n",
       "3                                0               0                              0             1                 0                       1                0  2068.0           0.042070    0.0    1.0   \n",
       "4                                0               0                              0             1                 0                       1                0  2068.0           0.085106    0.0    1.0   \n",
       "\n",
       "   REF_g  REF_t  ALT_a  ALT_c  ALT_g  ALT_t  \n",
       "0    1.0    0.0    0.0    1.0    0.0    0.0  \n",
       "1    1.0    0.0    0.0    0.0    0.0    1.0  \n",
       "2    1.0    0.0    0.0    1.0    0.0    0.0  \n",
       "3    0.0    0.0    0.0    0.0    0.0    1.0  \n",
       "4    0.0    0.0    0.0    0.0    0.0    1.0  "
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_nlp2.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 65188 entries, 0 to 65187\n",
      "Data columns (total 94 columns):\n",
      "POS                                65188 non-null int64\n",
      "REF                                65188 non-null object\n",
      "ALT                                65188 non-null object\n",
      "AF_ESP                             65188 non-null float64\n",
      "AF_EXAC                            65188 non-null float64\n",
      "AF_TGP                             65188 non-null float64\n",
      "CLNDISDB                           65188 non-null object\n",
      "CLNDISDBINCL                       76 non-null object\n",
      "CLNDN                              65188 non-null object\n",
      "CLNDNINCL                          76 non-null object\n",
      "CLNHGVS                            65188 non-null object\n",
      "CLNSIGINCL                         76 non-null object\n",
      "CLNVI                              27659 non-null object\n",
      "MC                                 58219 non-null object\n",
      "ORIGIN                             65188 non-null float64\n",
      "SSR                                65188 non-null float64\n",
      "CLASS                              65188 non-null int64\n",
      "Allele                             65188 non-null object\n",
      "Consequence                        65188 non-null object\n",
      "IMPACT                             65188 non-null object\n",
      "SYMBOL                             65172 non-null object\n",
      "Feature_type                       65174 non-null object\n",
      "Feature                            65174 non-null object\n",
      "EXON                               56295 non-null object\n",
      "INTRON                             8803 non-null object\n",
      "cDNA_position                      56304 non-null object\n",
      "CDS_position                       55233 non-null object\n",
      "Protein_position                   54027 non-null float64\n",
      "Amino_acids                        55184 non-null object\n",
      "Codons                             55184 non-null object\n",
      "DISTANCE                           108 non-null float64\n",
      "STRAND                             65188 non-null float64\n",
      "BAM_EDIT                           31969 non-null object\n",
      "PolyPhen                           24796 non-null object\n",
      "MOTIF_NAME                         2 non-null object\n",
      "MOTIF_POS                          2 non-null float64\n",
      "HIGH_INF_POS                       2 non-null object\n",
      "MOTIF_SCORE_CHANGE                 2 non-null float64\n",
      "LoFtool                            65188 non-null float64\n",
      "CADD_PHRED                         65188 non-null float64\n",
      "CADD_RAW                           65188 non-null float64\n",
      "BLOSUM62                           25593 non-null float64\n",
      "CHROM_1                            65188 non-null int64\n",
      "CHROM_2                            65188 non-null int64\n",
      "CHROM_3                            65188 non-null int64\n",
      "CHROM_4                            65188 non-null int64\n",
      "CHROM_5                            65188 non-null int64\n",
      "CHROM_6                            65188 non-null int64\n",
      "CHROM_7                            65188 non-null int64\n",
      "CHROM_8                            65188 non-null int64\n",
      "CHROM_9                            65188 non-null int64\n",
      "CHROM_10                           65188 non-null int64\n",
      "CHROM_11                           65188 non-null int64\n",
      "CHROM_12                           65188 non-null int64\n",
      "CHROM_13                           65188 non-null int64\n",
      "CHROM_14                           65188 non-null int64\n",
      "CHROM_15                           65188 non-null int64\n",
      "CHROM_16                           65188 non-null int64\n",
      "CHROM_16.1                         65188 non-null int64\n",
      "CHROM_17                           65188 non-null int64\n",
      "CHROM_18                           65188 non-null int64\n",
      "CHROM_19                           65188 non-null int64\n",
      "CHROM_20                           65188 non-null int64\n",
      "CHROM_21                           65188 non-null int64\n",
      "CHROM_22                           65188 non-null int64\n",
      "CHROM_MT                           65188 non-null int64\n",
      "CHROM_X                            65188 non-null int64\n",
      "CLNVC_Deletion                     65188 non-null int64\n",
      "CLNVC_Duplication                  65188 non-null int64\n",
      "CLNVC_Indel                        65188 non-null int64\n",
      "CLNVC_Insertion                    65188 non-null int64\n",
      "CLNVC_Inversion                    65188 non-null int64\n",
      "CLNVC_Microsatellite               65188 non-null int64\n",
      "CLNVC_single_nucleotide_variant    65188 non-null int64\n",
      "INT                                65188 non-null int64\n",
      "EX                                 65188 non-null int64\n",
      "SIFT_deleterious                   65188 non-null int64\n",
      "SIFT_deleterious_low_confidence    65188 non-null int64\n",
      "SIFT_tolerated                     65188 non-null int64\n",
      "SIFT_tolerated_low_confidence      65188 non-null int64\n",
      "SIFT_unknown                       65188 non-null int64\n",
      "BIOTYPE_misc_RNA                   65188 non-null int64\n",
      "BIOTYPE_protein_coding             65188 non-null int64\n",
      "BIOTYPE_unknown                    65188 non-null int64\n",
      "Length                             64995 non-null float64\n",
      "Relative_Location                  65188 non-null float64\n",
      "REF_a                              65188 non-null float64\n",
      "REF_c                              65188 non-null float64\n",
      "REF_g                              65188 non-null float64\n",
      "REF_t                              65188 non-null float64\n",
      "ALT_a                              65188 non-null float64\n",
      "ALT_c                              65188 non-null float64\n",
      "ALT_g                              65188 non-null float64\n",
      "ALT_t                              65188 non-null float64\n",
      "dtypes: float64(24), int64(44), object(26)\n",
      "memory usage: 46.8+ MB\n"
     ]
    }
   ],
   "source": [
    "df_nlp2.info()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Save the dataframe in a csv file\n",
    "df_nlp2.to_csv('data/data_cleanednlp4.csv', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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