{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "reset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Please run this code block only once, the first time you are running this notebook\n",
    "!pip3 install google.cloud"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "#To be able to retrieve data from google cloud bigquery tables \n",
    "from google.cloud import bigquery"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Go to the following link in your browser:\n",
      "\n",
      "    https://accounts.google.com/o/oauth2/auth?client_id=764086051850-6qr4p6gpi6hn506pt8ejuq83di341hur.apps.googleusercontent.com&redirect_uri=urn%3Aietf%3Awg%3Aoauth%3A2.0%3Aoob&scope=openid+https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fuserinfo.email+https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fcloud-platform+https%3A%2F%2Fwww.googleapis.com%2Fauth%2Faccounts.reauth&code_challenge=YersnwhVgYOV3cr4BZNoOv5q8zoGEPEK3l8Ll6lzqIk&code_challenge_method=S256&access_type=offline&response_type=code&prompt=select_account\n",
      "\n",
      "\n",
      "Enter verification code: ^C\n",
      "\n",
      "\n",
      "Command killed by keyboard interrupt\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# authentication in myBinder\n",
    "!./google-cloud-sdk/bin/gcloud auth application-default login\n",
    "\n",
    "# If you install google cloud sdk \n",
    "#!gcloud auth application-default login"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "project_id='syntheticlethality' #please replace syntheticlethality with your own projectid\n",
    "client = bigquery.Client(project_id)\n",
    "#client = bigquery.Client(credentials=credentials, project=credentials.project_id)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Retireve BRCA1 gene effect score of the first data entry for gene BRCA1 from CRISPR dataset\n",
    "crispr_query=\"\"\"\n",
    "SELECT * FROM \n",
    "`syntheticlethality.DepMap_public_20Q3.Achilles_gene_effect`\n",
    "WHERE Hugo_Symbol='BRCA1'\n",
    "LIMIT 10\n",
    "\"\"\"\n",
    "brca1_gene_effect=client.query(crispr_query).result().to_dataframe()\n",
    "brca1_gene_effect"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Retrieve the first 10 records for BRCA1 gene expression from pancancer atlas dataset\n",
    "pancancer_atlas_query=\"\"\"\n",
    "SELECT * FROM\n",
    "`pancancer-atlas.Filtered.EBpp_AdjustPANCAN_IlluminaHiSeq_RNASeqV2_genExp_filtered` \n",
    "WHERE Symbol='BRCA1'\n",
    "LIMIT 10\n",
    "\"\"\"\n",
    "brca1_gene_exp=client.query(pancancer_atlas_query).result().to_dataframe()\n",
    "brca1_gene_exp"
   ]
  }
 ],
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