minimal_jupyter.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from socialgene.neo4j.neo4j import GraphDriver\n",
    "from socialgene.config import env_vars\n",
    "import logging\n",
    "import os\n",
    "\n",
    "env_vars[\"NEO4J_URI\"] =\"bolt://localhost:7687\"\n",
    "os.environ[\"NEO4J_PASSWORD\"] = \"test12345\"\n",
    "logging.getLogger(\"neo4j\").setLevel(logging.WARNING)\n",
    "logging.getLogger().setLevel(logging.INFO)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "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>a1.uid</th>\n",
       "      <th>n1.external_id</th>\n",
       "      <th>antismash_region</th>\n",
       "      <th>antismash_products</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GCF_000145235.1</td>\n",
       "      <td>NC_014391.1</td>\n",
       "      <td>4</td>\n",
       "      <td>[NRPS, 2dos, T1PKS, NRPS-like]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>GCF_000145235.1</td>\n",
       "      <td>NC_014391.1</td>\n",
       "      <td>5</td>\n",
       "      <td>[T1PKS]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>GCF_000145235.1</td>\n",
       "      <td>NC_014391.1</td>\n",
       "      <td>8</td>\n",
       "      <td>[NRPS-like, NRPS, T1PKS]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GCF_000145235.1</td>\n",
       "      <td>NC_014391.1</td>\n",
       "      <td>7</td>\n",
       "      <td>[NRPS-like, NRPS, T1PKS, PKS-like]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>GCF_000158815.1</td>\n",
       "      <td>NZ_GG657738.1</td>\n",
       "      <td>17</td>\n",
       "      <td>[T1PKS]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>GCF_000158815.1</td>\n",
       "      <td>NZ_GG657738.1</td>\n",
       "      <td>13</td>\n",
       "      <td>[T1PKS, PKS-like, other, oligosaccharide]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>GCF_000158815.1</td>\n",
       "      <td>NZ_GG657738.1</td>\n",
       "      <td>4</td>\n",
       "      <td>[T1PKS]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>GCF_000158815.1</td>\n",
       "      <td>NZ_GG657738.1</td>\n",
       "      <td>20</td>\n",
       "      <td>[NRPS, T1PKS]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>GCF_000158815.1</td>\n",
       "      <td>NZ_GG657738.1</td>\n",
       "      <td>5</td>\n",
       "      <td>[arylpolyene, T1PKS]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>GCF_000158815.1</td>\n",
       "      <td>NZ_GG657738.1</td>\n",
       "      <td>7</td>\n",
       "      <td>[T1PKS]</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "            a1.uid n1.external_id  antismash_region  \\\n",
       "0  GCF_000145235.1    NC_014391.1                 4   \n",
       "1  GCF_000145235.1    NC_014391.1                 5   \n",
       "2  GCF_000145235.1    NC_014391.1                 8   \n",
       "3  GCF_000145235.1    NC_014391.1                 7   \n",
       "4  GCF_000158815.1  NZ_GG657738.1                17   \n",
       "5  GCF_000158815.1  NZ_GG657738.1                13   \n",
       "6  GCF_000158815.1  NZ_GG657738.1                 4   \n",
       "7  GCF_000158815.1  NZ_GG657738.1                20   \n",
       "8  GCF_000158815.1  NZ_GG657738.1                 5   \n",
       "9  GCF_000158815.1  NZ_GG657738.1                 7   \n",
       "\n",
       "                          antismash_products  \n",
       "0             [NRPS, 2dos, T1PKS, NRPS-like]  \n",
       "1                                    [T1PKS]  \n",
       "2                   [NRPS-like, NRPS, T1PKS]  \n",
       "3         [NRPS-like, NRPS, T1PKS, PKS-like]  \n",
       "4                                    [T1PKS]  \n",
       "5  [T1PKS, PKS-like, other, oligosaccharide]  \n",
       "6                                    [T1PKS]  \n",
       "7                              [NRPS, T1PKS]  \n",
       "8                       [arylpolyene, T1PKS]  \n",
       "9                                    [T1PKS]  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "with GraphDriver() as db:\n",
    "    results = db.run(\n",
    "        \"\"\"\n",
    "MATCH p=(a1:assembly)-[:ASSEMBLES_TO]-(n1:nucleotide)-[e1:ENCODES]->(p1:protein) \n",
    "WHERE 'T1PKS' IN  e1.antismash_products\n",
    "RETURN DISTINCT a1.uid, n1.external_id, e1.antismash_region as antismash_region, e1.antismash_products as antismash_products\n",
    "limit 10\n",
    "\"\"\"\n",
    "    ).to_df()\n",
    "\n",
    "results"
   ]
  }
 ],
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  "kernelspec": {
   "display_name": "sgpy",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.12.0"
  }
 },
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 "nbformat_minor": 2
}