get_one_hot_encoded_sequences.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "def oneHotEncodeSequence(sequence):\n",
    "    oneHotDimension = (len(sequence), 4)\n",
    "    dnaAlphabet = {\"A\":0, \"G\":1, \"C\":2, \"T\":3}\n",
    "    one_hot_encoded_sequence = np.zeros(oneHotDimension, dtype=np.int)\n",
    "    for i, nucleotide in enumerate(sequence):\n",
    "        if nucleotide.upper() in dnaAlphabet:\n",
    "            index = dnaAlphabet[nucleotide.upper()]\n",
    "            one_hot_encoded_sequence[i][index] = 1\n",
    "    return one_hot_encoded_sequence"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "snp_data = pd.read_csv(\"/projects/pfenninggroup/machineLearningForComputationalBiology/eramamur_stuff/ad_variants_processing/snigdha_snp_list_unique_haploreg_hg19_positions_1kb_and_500bp_sequences.txt\",\n",
    "                       header=0,\n",
    "                       sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "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>CHR</th>\n",
       "      <th>haploreg_hg19_pos</th>\n",
       "      <th>LD_RSID</th>\n",
       "      <th>REF</th>\n",
       "      <th>ALT</th>\n",
       "      <th>ref_1kb</th>\n",
       "      <th>alt_1kb</th>\n",
       "      <th>ref_500bp</th>\n",
       "      <th>alt_500bp</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>chr10</td>\n",
       "      <td>11707563</td>\n",
       "      <td>rs34388456</td>\n",
       "      <td>GCCT</td>\n",
       "      <td>G</td>\n",
       "      <td>taagggttcaagctctggggacccggtcccagggaatccccacact...</td>\n",
       "      <td>ctaagggttcaagctctggggacccggtcccagggaatccccacac...</td>\n",
       "      <td>ttgagtgcaatggcacgatcttggctcactgcaatctccgccttcc...</td>\n",
       "      <td>cttgagtgcaatggcacgatcttggctcactgcaatctccgccttc...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>chr10</td>\n",
       "      <td>11707915</td>\n",
       "      <td>rs11257227</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>taccaccatgcctggctaatttttgtatttttagtaaagacagggt...</td>\n",
       "      <td>taccaccatgcctggctaatttttgtatttttagtaaagacagggt...</td>\n",
       "      <td>ttctccttcttcttcttcttcctttagacaaggtcttgctcttctt...</td>\n",
       "      <td>ttctccttcttcttcttcttcctttagacaaggtcttgctcttctt...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>chr10</td>\n",
       "      <td>11714507</td>\n",
       "      <td>rs74347557</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>cttggtgccctgaaacaattactatagtaacagcgaagatcacaga...</td>\n",
       "      <td>cttggtgccctgaaacaattactatagtaacagcgaagatcacaga...</td>\n",
       "      <td>tgtgggcctggccgggcacggtggcttacgcctgtaatcccagcac...</td>\n",
       "      <td>tgtgggcctggccgggcacggtggcttacgcctgtaatcccagcac...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>chr10</td>\n",
       "      <td>11714686</td>\n",
       "      <td>rs77892763</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>gccacaaaccttccattttgtaaaaagtacaatatctgcaaagcac...</td>\n",
       "      <td>gccacaaaccttccattttgtaaaaagtacaatatctgcaaagcac...</td>\n",
       "      <td>tactagggaggctgaggcaggagaattgcttgaacccgggaggcag...</td>\n",
       "      <td>tactagggaggctgaggcaggagaattgcttgaacccgggaggcag...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>chr10</td>\n",
       "      <td>11717397</td>\n",
       "      <td>rs11257238</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>tcaaggaccctgccctcaagaagtttagagtctggaaagagacaca...</td>\n",
       "      <td>tcaaggaccctgccctcaagaagtttagagtctggaaagagacaca...</td>\n",
       "      <td>aggcaggagaatcacttgaacccaggaggcggaggttgcaatgtgc...</td>\n",
       "      <td>aggcaggagaatcacttgaacccaggaggcggaggttgcaatgtgc...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     CHR  haploreg_hg19_pos     LD_RSID   REF ALT  \\\n",
       "0  chr10           11707563  rs34388456  GCCT   G   \n",
       "1  chr10           11707915  rs11257227     A   G   \n",
       "2  chr10           11714507  rs74347557     C   T   \n",
       "3  chr10           11714686  rs77892763     C   T   \n",
       "4  chr10           11717397  rs11257238     T   C   \n",
       "\n",
       "                                             ref_1kb  \\\n",
       "0  taagggttcaagctctggggacccggtcccagggaatccccacact...   \n",
       "1  taccaccatgcctggctaatttttgtatttttagtaaagacagggt...   \n",
       "2  cttggtgccctgaaacaattactatagtaacagcgaagatcacaga...   \n",
       "3  gccacaaaccttccattttgtaaaaagtacaatatctgcaaagcac...   \n",
       "4  tcaaggaccctgccctcaagaagtttagagtctggaaagagacaca...   \n",
       "\n",
       "                                             alt_1kb  \\\n",
       "0  ctaagggttcaagctctggggacccggtcccagggaatccccacac...   \n",
       "1  taccaccatgcctggctaatttttgtatttttagtaaagacagggt...   \n",
       "2  cttggtgccctgaaacaattactatagtaacagcgaagatcacaga...   \n",
       "3  gccacaaaccttccattttgtaaaaagtacaatatctgcaaagcac...   \n",
       "4  tcaaggaccctgccctcaagaagtttagagtctggaaagagacaca...   \n",
       "\n",
       "                                           ref_500bp  \\\n",
       "0  ttgagtgcaatggcacgatcttggctcactgcaatctccgccttcc...   \n",
       "1  ttctccttcttcttcttcttcctttagacaaggtcttgctcttctt...   \n",
       "2  tgtgggcctggccgggcacggtggcttacgcctgtaatcccagcac...   \n",
       "3  tactagggaggctgaggcaggagaattgcttgaacccgggaggcag...   \n",
       "4  aggcaggagaatcacttgaacccaggaggcggaggttgcaatgtgc...   \n",
       "\n",
       "                                           alt_500bp  \n",
       "0  cttgagtgcaatggcacgatcttggctcactgcaatctccgccttc...  \n",
       "1  ttctccttcttcttcttcttcctttagacaaggtcttgctcttctt...  \n",
       "2  tgtgggcctggccgggcacggtggcttacgcctgtaatcccagcac...  \n",
       "3  tactagggaggctgaggcaggagaattgcttgaacccgggaggcag...  \n",
       "4  aggcaggagaatcacttgaacccaggaggcggaggttgcaatgtgc...  "
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "snp_data.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "encodedRefSequences_1kb = []\n",
    "encodedAltSequences_1kb = []\n",
    "encodedRefSequences_500bp = []\n",
    "encodedAltSequences_500bp = []\n",
    "\n",
    "ref_1kb_output = \"/projects/pfenninggroup/machineLearningForComputationalBiology/eramamur_stuff/ad_variants_processing/ref_1kb_sequences.npy\"    \n",
    "alt_1kb_output = \"/projects/pfenninggroup/machineLearningForComputationalBiology/eramamur_stuff/ad_variants_processing/alt_1kb_sequences.npy\"    \n",
    "ref_500bp_output = \"/projects/pfenninggroup/machineLearningForComputationalBiology/eramamur_stuff/ad_variants_processing/ref_500bp_sequences.npy\"  \n",
    "alt_500bp_output = \"/projects/pfenninggroup/machineLearningForComputationalBiology/eramamur_stuff/ad_variants_processing/alt_500bp_sequences.npy\"  \n",
    "\n",
    "\n",
    "for index,row in snp_data.iterrows():\n",
    "    refSequence_1kb = row[\"ref_1kb\"]\n",
    "    altSequence_1kb = row[\"alt_1kb\"]\n",
    "    refSequence_500bp = row[\"ref_500bp\"]\n",
    "    altSequence_500bp = row[\"alt_500bp\"]\n",
    "    \n",
    "    encodedRefSequences_1kb.append(oneHotEncodeSequence(refSequence_1kb))\n",
    "    encodedAltSequences_1kb.append(oneHotEncodeSequence(altSequence_1kb))\n",
    "    encodedRefSequences_500bp.append(oneHotEncodeSequence(refSequence_500bp))\n",
    "    encodedAltSequences_500bp.append(oneHotEncodeSequence(altSequence_500bp))\n",
    "    \n",
    "encodedRefSequences_1kb = np.stack(encodedRefSequences_1kb, axis=0)\n",
    "encodedAltSequences_1kb = np.stack(encodedAltSequences_1kb, axis=0)\n",
    "encodedRefSequences_500bp = np.stack(encodedRefSequences_500bp, axis=0)\n",
    "encodedAltSequences_500bp = np.stack(encodedAltSequences_500bp, axis=0)\n",
    "\n",
    "\n",
    "np.save(ref_1kb_output, encodedRefSequences_1kb)\n",
    "np.save(alt_1kb_output, encodedAltSequences_1kb)\n",
    "np.save(ref_500bp_output, encodedRefSequences_500bp)\n",
    "np.save(alt_500bp_output, encodedAltSequences_500bp)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(1209, 1000, 4)\n",
      "(1209, 1000, 4)\n",
      "(1209, 500, 4)\n",
      "(1209, 500, 4)\n"
     ]
    }
   ],
   "source": [
    "print encodedRefSequences_1kb.shape\n",
    "print encodedAltSequences_1kb.shape\n",
    "print encodedRefSequences_500bp.shape\n",
    "print encodedAltSequences_500bp.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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