{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/saketkc/pysradb/blob/develop/notebooks/06.Multiple_SRPs.ipynb)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Querying Multiple Projects\n",
    "\n",
    "This notebook demonstrates how to query and export metadata from multiple SRA projects at once."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Install pysradb if not already installed\n",
    "try:\n",
    "    import pysradb\n",
    "\n",
    "    print(f\"pysradb {pysradb.__version__} is already installed\")\n",
    "except ImportError:\n",
    "    print(\"Installing pysradb from GitHub...\")\n",
    "    import sys\n",
    "\n",
    "    !{sys.executable} -m pip install -q git+https://github.com/saketkc/pysradb\n",
    "    print(\"pysradb installed successfully!\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/",
     "height": 401
    },
    "colab_type": "code",
    "id": "kPEeKLC38WGX",
    "outputId": "45055cff-1f41-4b1d-f67f-0a4dc37a8333"
   },
   "outputs": [],
   "source": [
    "# pip install git+https://github.com/saketkc/pysradb.git"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "colab": {},
    "colab_type": "code",
    "id": "n-lUysUE8edh"
   },
   "outputs": [],
   "source": [
    "SRP_list = \"\"\"ERP009675\n",
    "ERP007116\n",
    "ERP007115\n",
    "ERP004563\n",
    "ERP005660\n",
    "ERP001266\n",
    "ERP002072\n",
    "ERP001882\n",
    "ERP004883\n",
    "ERP004508\n",
    "ERP004393\n",
    "ERP005409\n",
    "ERP001464\n",
    "ERP004042\n",
    "ERP004375\n",
    "ERP003293\n",
    "ERP004689\n",
    "ERP001094\n",
    "ERP003728\n",
    "ERP000730\n",
    "ERP000411\n",
    "ERP000319\n",
    "SRP041183\n",
    "SRP011912\n",
    "SRP058392\n",
    "SRP044705\n",
    "SRP036841\n",
    "SRP050120\n",
    "ERP004116\n",
    "SRP030662\n",
    "SRP047217\n",
    "SRP045505\n",
    "ERP001556\n",
    "ERP000546\n",
    "SRP045252\n",
    "SRP044714\n",
    "DRP000524\n",
    "SRP044907\n",
    "SRP019970\n",
    "SRP044131\n",
    "SRP044042\n",
    "SRP043602\n",
    "SRP043523\n",
    "SRP014570\n",
    "SRP043067\n",
    "SRP042370\n",
    "SRP042360\n",
    "SRP042159\n",
    "SRP042085\n",
    "SRP042053\n",
    "SRP041992\n",
    "SRP041738\n",
    "SRP041679\n",
    "SRP041669\n",
    "SRP041622\n",
    "SRP041182\n",
    "SRP041377\n",
    "SRP021009\n",
    "SRP041216\n",
    "SRP041129\n",
    "SRP041119\n",
    "SRP041044\n",
    "SRP040761\n",
    "SRP040479\n",
    "SRP040072\n",
    "SRP040070\n",
    "SRP040121\n",
    "SRP040044\n",
    "SRP039841\n",
    "SRP039779\n",
    "SRP039717\n",
    "SRP039699\n",
    "SRP039672\n",
    "SRP039661\n",
    "SRP039646\n",
    "SRP039634\n",
    "SRP035451\n",
    "SRP039551\n",
    "SRP039478\n",
    "SRP039440\n",
    "SRP039448\n",
    "SRP030474\n",
    "SRP034507\n",
    "SRP038004\n",
    "SRP037780\n",
    "SRP037583\n",
    "SRP036068\n",
    "SRP036637\n",
    "SRP036632\n",
    "SRP035368\n",
    "SRP035278\n",
    "SRP034930\n",
    "SRP034844\n",
    "ERP004159\n",
    "SRP017087\n",
    "SRP034444\n",
    "SRP033229\n",
    "SRP033198\n",
    "SRP033021\n",
    "ERP000964\n",
    "ERP002429\n",
    "SRP032928\n",
    "SRP032833\n",
    "SRP032792\n",
    "SRP032766\n",
    "ERP003855\n",
    "ERP000904\n",
    "SRP028229\n",
    "SRP026361\n",
    "SRP023111\n",
    "SRP021139\n",
    "SRP013319\n",
    "SRP020006\n",
    "SRP019994\n",
    "SRP019500\n",
    "SRP019241\n",
    "SRP018672\n",
    "SRP018358\n",
    "SRP016875\n",
    "SRP016501\n",
    "SRP015460\n",
    "SRP015370\n",
    "SRP015135\n",
    "SRP014437\n",
    "SRP012378\n",
    "SRP012018\n",
    "SRP010103\n",
    "SRP007831\n",
    "SRP007412\n",
    "SRP007400\n",
    "SRP002090\n",
    "SRP029153\n",
    "SRP029445\n",
    "SRP029427\n",
    "SRP029380\n",
    "SRP029330\n",
    "SRP029333\n",
    "ERP000606\n",
    "ERP000415\n",
    "ERP001977\n",
    "ERP000373\n",
    "SRP029172\n",
    "SRP028766\n",
    "ERP000668\n",
    "ERP003627\n",
    "SRP017364\n",
    "SRP025757\n",
    "SRP021189\n",
    "SRP011154\n",
    "SRP014574\n",
    "SRP017935\n",
    "SRP016889\n",
    "SRP002016\n",
    "SRP018826\n",
    "SRP018753\n",
    "SRP009821\n",
    "SRP012925\n",
    "SRP012850\n",
    "SRP009870\n",
    "SRP007799\n",
    "SRP006748\n",
    "SRP000373\"\"\"\n",
    "SRP_list = SRP_list.split(\"\\n\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/",
     "height": 72
    },
    "colab_type": "code",
    "id": "1CWmd5rF8yny",
    "outputId": "519c91be-e3b9-48a3-fd47-fbe415bd0b2a"
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/saket/miniforge3/lib/python3.12/site-packages/pysradb/utils.py:14: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n",
      "  from tqdm.autonotebook import tqdm\n",
      "Error with SRP045252\n"
     ]
    }
   ],
   "source": [
    "import sys\n",
    "import time\n",
    "\n",
    "from pysradb import SRAweb\n",
    "\n",
    "db = SRAweb()\n",
    "\n",
    "for srp in SRP_list:\n",
    "    try:\n",
    "        df = db.sra_metadata(srp)\n",
    "        df.to_csv(\"{}.tsv\".format(srp), sep=\"\\t\", index=False)\n",
    "    except:\n",
    "        sys.stderr.write(\"Error with {}\\n\".format(srp))\n",
    "        time.sleep(0.5)\n",
    "    time.sleep(0.5)"
   ]
  }
 ],
 "metadata": {
  "colab": {
   "authorship_tag": "ABX9TyMmcvA8kJPyf4bhs59mCISs",
   "include_colab_link": true,
   "mount_file_id": "1pNeuZJjjHliYFk582kGNRpGJ1Fa2h9cn",
   "name": "07.Multiple_SRPs",
   "provenance": []
  },
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
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  "language_info": {
   "codemirror_mode": {
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   "file_extension": ".py",
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