svif-results.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "5fef58fd-5e82-4993-b073-0759bae14464",
   "metadata": {},
   "source": [
    "## [ Indonesian Rice SNPs - Information Content Pre-analysis ]\n",
    "`Prepared by` <b>Nicholas Dominic, S.Kom., M.T.I.</b>"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "373501d4-057e-4b68-aeea-44322f62fdb3",
   "metadata": {},
   "source": [
    "### Define libraries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "6cb891fd-98d4-4772-8b86-8fc2c59dbccc",
   "metadata": {},
   "outputs": [],
   "source": [
    "from pandas import read_csv, DataFrame\n",
    "from os import listdir"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "499a1962-0519-4303-94f7-67072b196114",
   "metadata": {},
   "source": [
    "### Load raw SNPs data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "2bdaba49-49e9-4694-b1dc-871220209604",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "    }\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>id</th>\n",
       "      <th>posg</th>\n",
       "      <th>pos</th>\n",
       "      <th>ref</th>\n",
       "      <th>alt</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1</td>\n",
       "      <td>id1000223</td>\n",
       "      <td>0</td>\n",
       "      <td>422620</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1</td>\n",
       "      <td>id1001073</td>\n",
       "      <td>0</td>\n",
       "      <td>1174585</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1</td>\n",
       "      <td>id1001973</td>\n",
       "      <td>0</td>\n",
       "      <td>2568541</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1</td>\n",
       "      <td>id1002158</td>\n",
       "      <td>0</td>\n",
       "      <td>2725468</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>1</td>\n",
       "      <td>id1002308</td>\n",
       "      <td>0</td>\n",
       "      <td>2899077</td>\n",
       "      <td>C</td>\n",
       "      <td>T</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1393</th>\n",
       "      <td>12</td>\n",
       "      <td>id12009153</td>\n",
       "      <td>0</td>\n",
       "      <td>25558936</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1394</th>\n",
       "      <td>12</td>\n",
       "      <td>id12009407</td>\n",
       "      <td>0</td>\n",
       "      <td>26057332</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1395</th>\n",
       "      <td>12</td>\n",
       "      <td>id12009654</td>\n",
       "      <td>0</td>\n",
       "      <td>26360367</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1396</th>\n",
       "      <td>12</td>\n",
       "      <td>id12009820</td>\n",
       "      <td>0</td>\n",
       "      <td>26873949</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1397</th>\n",
       "      <td>12</td>\n",
       "      <td>id12010152</td>\n",
       "      <td>0</td>\n",
       "      <td>27728824</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1397 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      chr          id  posg       pos ref alt\n",
       "1       1   id1000223     0    422620   T   G\n",
       "2       1   id1001073     0   1174585   G   A\n",
       "3       1   id1001973     0   2568541   T   C\n",
       "4       1   id1002158     0   2725468   T   C\n",
       "5       1   id1002308     0   2899077   C   T\n",
       "...   ...         ...   ...       ...  ..  ..\n",
       "1393   12  id12009153     0  25558936   A   G\n",
       "1394   12  id12009407     0  26057332   C   T\n",
       "1395   12  id12009654     0  26360367   A   G\n",
       "1396   12  id12009820     0  26873949   T   C\n",
       "1397   12  id12010152     0  27728824   T   C\n",
       "\n",
       "[1397 rows x 6 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "raw_snps = read_csv(\"data/ind-rg.csv\", index_col=0)\n",
    "raw_snps"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7eeb89b3-899c-464b-9a35-32dea1936948",
   "metadata": {},
   "source": [
    "### Get SVIF result path and files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "1ee82326-4d9e-4100-86f8-6ec503bbf454",
   "metadata": {},
   "outputs": [],
   "source": [
    "RESULT_PATH = \"results/svif/\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "43d6bed2-0ab7-434f-9ad6-be24eb1b8ad2",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{0: 'results/svif/chr-10_(thresh-2.5).csv',\n",
       " 1: 'results/svif/chr-11_(thresh-2.5).csv',\n",
       " 2: 'results/svif/chr-12_(thresh-2.5).csv',\n",
       " 3: 'results/svif/chr-1_(thresh-2.5).csv',\n",
       " 4: 'results/svif/chr-2_(thresh-2.5).csv',\n",
       " 5: 'results/svif/chr-3_(thresh-2.5).csv',\n",
       " 6: 'results/svif/chr-4_(thresh-2.5).csv',\n",
       " 7: 'results/svif/chr-5_(thresh-2.5).csv',\n",
       " 8: 'results/svif/chr-6_(thresh-2.5).csv',\n",
       " 9: 'results/svif/chr-7_(thresh-2.5).csv',\n",
       " 10: 'results/svif/chr-8_(thresh-2.5).csv',\n",
       " 11: 'results/svif/chr-9_(thresh-2.5).csv'}"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "result = [RESULT_PATH+x for x in listdir(RESULT_PATH) if x.endswith(\".csv\")]\n",
    "{file_num : r for file_num, r in enumerate(result)}"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7108e7f5-c6e5-4a8f-a2da-52c3c4e504bc",
   "metadata": {},
   "source": [
    "### Declare neccessary function"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "20b684cb-86da-49e1-b911-daa4d4c4aa46",
   "metadata": {},
   "outputs": [],
   "source": [
    "def analyze_pos(select_file_num : int = 0, *args, **kwargs) -> DataFrame:\n",
    "    chr_num = int(result[select_file_num].split(\"chr-\")[1].split(\"_\")[0])\n",
    "    print(\"Analyzing SVIF result from chromosome {} ...\".format(chr_num))\n",
    "    \n",
    "    selected_chr = raw_snps[raw_snps.chr == chr_num]\n",
    "    id_ref = list(map('_'.join, zip(selected_chr.id.values.tolist(), selected_chr.ref.values.tolist())))\n",
    "    selected_chr.insert(len(selected_chr.columns), \"id_ref\", id_ref)\n",
    "    \n",
    "    svif_result = read_csv(result[select_file_num])\n",
    "    return svif_result.merge(selected_chr, left_on=\"SNP\", right_on=\"id_ref\")[[\"SNP\", \"agg_count\", \"pos\"]]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "08863e75-ac14-45fb-865c-a13c978a7717",
   "metadata": {},
   "source": [
    "### Get SNP position"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "9e082410-b373-40ed-bfa0-e841dba2cd17",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Analyzing SVIF result from chromosome 1 ...\n"
     ]
    },
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>SNP</th>\n",
       "      <th>agg_count</th>\n",
       "      <th>pos</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TBGI040340_T</td>\n",
       "      <td>5</td>\n",
       "      <td>24597159</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TBGI052052_G</td>\n",
       "      <td>5</td>\n",
       "      <td>31851695</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TBGI049455_G</td>\n",
       "      <td>5</td>\n",
       "      <td>30423222</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>TBGI048143_G</td>\n",
       "      <td>5</td>\n",
       "      <td>29839335</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>TBGI048670_T</td>\n",
       "      <td>5</td>\n",
       "      <td>30094526</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>id1015931_A</td>\n",
       "      <td>5</td>\n",
       "      <td>29313930</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>TBGI044811_A</td>\n",
       "      <td>5</td>\n",
       "      <td>28000988</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>TBGI044294_A</td>\n",
       "      <td>5</td>\n",
       "      <td>27505528</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>id1012666_A</td>\n",
       "      <td>5</td>\n",
       "      <td>23995074</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>TBGI046808_C</td>\n",
       "      <td>5</td>\n",
       "      <td>28971365</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "            SNP  agg_count       pos\n",
       "0  TBGI040340_T          5  24597159\n",
       "1  TBGI052052_G          5  31851695\n",
       "2  TBGI049455_G          5  30423222\n",
       "3  TBGI048143_G          5  29839335\n",
       "4  TBGI048670_T          5  30094526\n",
       "5   id1015931_A          5  29313930\n",
       "6  TBGI044811_A          5  28000988\n",
       "7  TBGI044294_A          5  27505528\n",
       "8   id1012666_A          5  23995074\n",
       "9  TBGI046808_C          5  28971365"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "select_file_num = 3 # change here, must be INT\n",
    "analyze_pos(select_file_num).head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "8f1a25b0-3797-4367-a260-be951c22e3dd",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Analyzing SVIF result from chromosome 10 ...\n"
     ]
    },
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>SNP</th>\n",
       "      <th>agg_count</th>\n",
       "      <th>pos</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>id10002180_C</td>\n",
       "      <td>5</td>\n",
       "      <td>6543844</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>id10002406_A</td>\n",
       "      <td>5</td>\n",
       "      <td>7254303</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TBGI406425_A</td>\n",
       "      <td>5</td>\n",
       "      <td>14570693</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>TBGI406289_G</td>\n",
       "      <td>5</td>\n",
       "      <td>14507149</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>id10002660_G</td>\n",
       "      <td>5</td>\n",
       "      <td>9918841</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>id10002329_A</td>\n",
       "      <td>5</td>\n",
       "      <td>7002473</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>id10003462_G</td>\n",
       "      <td>5</td>\n",
       "      <td>13539364</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>TBGI405706_A</td>\n",
       "      <td>5</td>\n",
       "      <td>13960740</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>TBGI405262_C</td>\n",
       "      <td>5</td>\n",
       "      <td>13379366</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>id10000350_G</td>\n",
       "      <td>4</td>\n",
       "      <td>1657153</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>id10002779_A</td>\n",
       "      <td>1</td>\n",
       "      <td>10607086</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "             SNP  agg_count       pos\n",
       "0   id10002180_C          5   6543844\n",
       "1   id10002406_A          5   7254303\n",
       "2   TBGI406425_A          5  14570693\n",
       "3   TBGI406289_G          5  14507149\n",
       "4   id10002660_G          5   9918841\n",
       "5   id10002329_A          5   7002473\n",
       "6   id10003462_G          5  13539364\n",
       "7   TBGI405706_A          5  13960740\n",
       "8   TBGI405262_C          5  13379366\n",
       "9   id10000350_G          4   1657153\n",
       "10  id10002779_A          1  10607086"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "select_file_num = 0 # change here, must be INT\n",
    "analyze_pos(select_file_num)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "61d4ce72-c328-4ed6-9d26-d148007dfa3d",
   "metadata": {},
   "source": [
    "### Copyright 2022 Authors\n",
    "* Do <b>NOT</b> use or redistribute this file <b>EXCEPT</b> there is an official permission from authors.\n",
    "* Please cite our paper whenever you take references from this research.\n",
    "* Any questions can be addressed to `nicholas.dominic@binus.ac.id` or `bdsrc@binus.edu`.\n",
    "\n",
    "Bioinformatics and Data Science Research Center [(visit page)](https://research.binus.ac.id/bdsrc/)\n",
    "<br>NVIDIA - BINUS Artificial Intelligence Research and Development Center [(visit page)](https://research.binus.ac.id/airdc/)\n",
    "<br><b>BINUS Higher Education</b>, part of BINUS Group [(visit page)](https://www.binus.edu/) [(visit QS page)](https://www.topuniversities.com/universities/bina-nusantara-university-binus)"
   ]
  }
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