{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import seaborn as sns\n",
    "import matplotlib.pyplot as plt\n",
    "from sqlalchemy import create_engine\n",
    "from sklearn import preprocessing\n",
    "import mysql.connector\n",
    "from pandas import DataFrame"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "triplets_total = pd.read_excel('./Data/Input/DISNET/triples_drebiop_final_dos.xlsx',engine='openpyxl')\n",
    "triplets_total = triplets_total.drop(columns=['Unnamed: 0'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "triplets_total = triplets_total.drop_duplicates()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "disease_one = triplets_total[[\"Original Condition CUI\"]]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "disease_one = disease_one.rename(columns={\"Original Condition CUI\": \"disease_id\"})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# genes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "genes = pd.read_excel((\"./Data/Input/DISNET/dis_gen.xlsx\"),engine='openpyxl')\n",
    "genes = gen.drop([\"Unnamed: 0\"],axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_gene = disease_one.merge(genes, how= \"inner\", on= \"disease_id\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_gen_num_gen = dis_gene.groupby(['disease_id']).count()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_gen_num_gen = dis_gen_num_gen.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "count     23.000000\n",
       "mean     105.130435\n",
       "std      149.308194\n",
       "min        2.000000\n",
       "25%       17.500000\n",
       "50%       37.000000\n",
       "75%       91.500000\n",
       "max      526.000000\n",
       "Name: gene_id, dtype: float64"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dis_gen_num_gen[\"gene_id\"].describe()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "#### pw via gene"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pw_gene = pd.read_csv('./Data/Input/DISNET/pathways_genes.tsv', sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_pw_gen = disease_one.merge(pw_gene, how= \"inner\", on= \"disease_id\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_pw_gen = dis_pw_gen.groupby(['disease_id']).count()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_pw_gen = dis_pw_gen.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "391.04347826086956"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dis_pw_gen[\"pathway_id\"].mean()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "#### pw direct"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_path_direct = pd.read_csv('./Data/Input/DISNET/disease_pathway.tsv', sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "dr_pw = disease_one.merge(dis_path_direct,on=\"disease_id\",how= \"inner\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "dr_pw = dr_pw.groupby(['disease_id']).count()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "dr_pw = dr_pw.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "nan"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dr_pw[\"pathway_id\"].mean()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "### drug"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "drug = pd.read_csv('./Data/Input/DISNET/drugs.tsv', sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_drug = disease_one.merge(drug, how= \"inner\", on= \"disease_id\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_drug = dis_drug.groupby(['disease_id']).count()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_drug = dis_drug.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "384.6"
      ]
     },
     "execution_count": 35,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dis_drug[\"drug_id\"].mean()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "### symptom"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sint = pd.read_csv('./Data/Input/DISNET/sint_all.tsv', sep='\\t')\n",
    "sint = sint.drop([\"Unnamed: 0\"],axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_sint = disease_one.merge(sint, how= \"inner\", on= \"disease_id\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_sint = dis_sint.groupby(['disease_id']).count()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_sint = dis_sint.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "68.6086956521739"
      ]
     },
     "execution_count": 40,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dis_sint[\"symptom\"].mean()"
   ]
  }
 ],
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