read, sort, save .parquet file with DuckDB

parquet_sort(DuckDB).ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import duckdb\n",
    "\n",
    "# Connect to DuckDB in-memory database\n",
    "con = duckdb.connect()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 3min 59s, sys: 53.1 s, total: 4min 52s\n",
      "Wall time: 2min 33s\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<duckdb.duckdb.DuckDBPyConnection at 0x2aed4b899ef0>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%%time\n",
    "\n",
    "input_file = 'NIPBL_R1.parquet'\n",
    "output_file = 'NIPBL_R1_sorted_duckdb.parquet'\n",
    "schema = \"\"\"\n",
    "    read_id: VARCHAR,\n",
    "    chrom1: VARCHAR,\n",
    "    pos1: BIGINT,\n",
    "    chrom2: VARCHAR,\n",
    "    pos2: BIGINT,\n",
    "    strand1: VARCHAR,\n",
    "    strand2: VARCHAR,\n",
    "    pairs_type: VARCHAR\n",
    "\"\"\"\n",
    "con.execute(f\"\"\"\n",
    "    COPY (\n",
    "        SELECT CAST(read_id AS VARCHAR), CAST(chrom1 AS VARCHAR), \n",
    "           CAST(pos1 AS BIGINT), CAST(chrom2 AS VARCHAR), \n",
    "           CAST(pos2 AS BIGINT), CAST(strand1 AS VARCHAR),\n",
    "           CAST(strand2 AS VARCHAR), CAST(pairs_type AS VARCHAR)\n",
    "        FROM read_parquet('{input_file}')\n",
    "        WHERE read_id NOT LIKE '#%'  -- Filter out lines that start with '#samheader'\n",
    "        ORDER BY chrom1, chrom2, pos1, pos2\n",
    "    ) TO '{output_file}' (FORMAT PARQUET);\n",
    "\"\"\")\n",
    "\n"
   ]
  }
 ],
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