Transform activity ChEMBL query results to DataFrame - first element twice?

chembl_activity.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Activities from ChEMBL from list of ChEMBL IDs"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Goal**: Get all bioactivity data linked to a list of ChEMBL IDs.\n",
    "\n",
    "**Problem**: When transforming the query result to a `pandas.DataFrame`, the first ChEMBL ID appears twice in the DataFrame."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/dominique/anaconda3/envs/teachopencadd/lib/python3.6/site-packages/grequests.py:21: MonkeyPatchWarning: Monkey-patching ssl after ssl has already been imported may lead to errors, including RecursionError on Python 3.6. It may also silently lead to incorrect behaviour on Python 3.7. Please monkey-patch earlier. See https://github.com/gevent/gevent/issues/1016. Modules that had direct imports (NOT patched): ['urllib3.contrib.pyopenssl (/home/dominique/anaconda3/envs/teachopencadd/lib/python3.6/site-packages/urllib3/contrib/pyopenssl.py)']. \n",
      "  curious_george.patch_all(thread=False, select=False)\n"
     ]
    }
   ],
   "source": [
    "from chembl_webresource_client.new_client import new_client\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Set ChEMBL activity client"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "activity = new_client.activity"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Get activities for a list of ChEMBL IDs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "activities = activity.filter(\n",
    "    molecule_chembl_id__in = ['CHEMBL2064599', 'CHEMBL520734'],\n",
    "    type = 'IC50', \n",
    "    relation = '=', \n",
    "    assay_type = 'B'\n",
    ").only(\n",
    "    'molecule_chembl_id'\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(activities)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[{'molecule_chembl_id': 'CHEMBL520734'}, {'molecule_chembl_id': 'CHEMBL520734'}]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "activities"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "chembl_webresource_client.query_set.QuerySet"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "type(activities)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Transform activity results to DataFrame"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "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",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>molecule_chembl_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CHEMBL520734</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CHEMBL520734</td>\n",
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       "      <th>2</th>\n",
       "      <td>CHEMBL520734</td>\n",
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      "text/plain": [
       "  molecule_chembl_id\n",
       "0       CHEMBL520734\n",
       "1       CHEMBL520734\n",
       "2       CHEMBL520734"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.DataFrame.from_records(activities)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Why does the first element of the list `molecule_chembl_id__in` occur twice when the activity query result (`QuerySet`) `activities` is transformed into a DataFrame?"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Workaround: Assign `QuerySet` to `list`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>molecule_chembl_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CHEMBL520734</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CHEMBL520734</td>\n",
       "    </tr>\n",
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      ],
      "text/plain": [
       "  molecule_chembl_id\n",
       "0       CHEMBL520734\n",
       "1       CHEMBL520734"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.DataFrame.from_records(list(activities))"
   ]
  }
 ],
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