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  {
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   "id": "9tcjtJ8cvaPv",
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   "source": [
    "# Simple query to OcéanIA Platform TARA_A100000171\n",
    "## This example shows how to extract arbitrary biological sub-sequences from a FASTA file available in the OcéanIA Platform"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5ea0f4b3",
   "metadata": {},
   "source": [
    "### 1. Prepare request params"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "4132badf",
   "metadata": {},
   "outputs": [],
   "source": [
    "TARA_SAMPLE_ID = \"TARA_A100000171\"\n",
    "\n",
    "# REQUEST_PARAMS is a list of tuples that identify subsequences to extract\n",
    "# each tuple must have the values (sequence_id, start_index, stop_index, sequence_type)\n",
    "# sequence type accepted values are [raw, complement, reverse_complement], optional value if ommited defaults to \"raw\".\n",
    "REQUEST_PARAMS = [\n",
    "            (\"TARA_A100000171_G_scaffold48_1\", 10, 50, \"complement\"),\n",
    "            (\"TARA_A100000171_G_scaffold48_1\", 10, 50),\n",
    "            (\"TARA_A100000171_G_scaffold48_1\", 10, 50, \"reverse_complement\"),\n",
    "            (\"TARA_A100000171_G_scaffold181_1\", 0, 50),\n",
    "            (\"TARA_A100000171_G_scaffold181_1\", 100, 200),\n",
    "            (\"TARA_A100000171_G_scaffold181_1\", 200, 230),\n",
    "            (\"TARA_A100000171_G_scaffold493_2\", 54, 76),\n",
    "            (\"TARA_A100000171_G_scaffold50396_2\", 87, 105),\n",
    "            (\"TARA_A100000171_G_C2001995_1\", 20, 635),\n",
    "            (\"TARA_A100000171_G_C2026460_1\", 0, 100),\n",
    "        ]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0159d5e7",
   "metadata": {},
   "source": [
    "### 2. Perform call to the OcéanIA services"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "6344f9c6",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[30-06-2021 07:58:00] Sending request for fasta sequences\n",
      "[30-06-2021 07:58:01] Request accepted\n",
      "[30-06-2021 07:58:01] Waiting for results...\n",
      "[30-06-2021 07:59:38] Done. Elapsed time: 98.09430822399736 seconds\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Result loaded into a DataFrame\n",
      "                                  id  start  end                type  \\\n",
      "0     TARA_A100000171_G_scaffold48_1     10   50          complement   \n",
      "1     TARA_A100000171_G_scaffold48_1     10   50                 raw   \n",
      "2     TARA_A100000171_G_scaffold48_1     10   50  reverse_complement   \n",
      "3    TARA_A100000171_G_scaffold181_1      0   50                 raw   \n",
      "4    TARA_A100000171_G_scaffold181_1    100  200                 raw   \n",
      "5    TARA_A100000171_G_scaffold181_1    200  230                 raw   \n",
      "6    TARA_A100000171_G_scaffold493_2     54   76                 raw   \n",
      "7  TARA_A100000171_G_scaffold50396_2     87  105                 raw   \n",
      "8       TARA_A100000171_G_C2001995_1     20  635                 raw   \n",
      "9       TARA_A100000171_G_C2026460_1      0  100                 raw   \n",
      "\n",
      "                                            sequence  \n",
      "0           ACCGTAACGTAGGCCATATTATTTTCATGGTCTTCCACAA  \n",
      "1           TGGCATTGCATCCGGTATAATAAAAGTACCAGAAGGTGTT  \n",
      "2           AACACCTTCTGGTACTTTTATTATACCGGATGCAATGCCA  \n",
      "3  CCAAGACCAAGCAATTTTAACACCACACTTAGATACTGCGCAAACA...  \n",
      "4  ATTATGTTACCAGCACTTGATAACCAAAAAGTTTGGGcaggattaa...  \n",
      "5                     ATCAAACTGATGCTACTAACTCAGAAGCAT  \n",
      "6                             TAAGTTTTTATTATTATATTTT  \n",
      "7                                 AGCTGTTCGGAAAACTAG  \n",
      "8  ACAGCACACCAAGCAGGTCGTCGACCGAAACGATATTGAGAAGAAT...  \n",
      "9  AATTTGAAACAACCCTAAAGTGTTTACCATAATAGGTTCTTAAATC...  \n"
     ]
    }
   ],
   "source": [
    "#@title Double click to see the cell of the Python program\n",
    "\n",
    "from oceania import get_sequences_from_fasta\n",
    "\n",
    "request_result = get_sequences_from_fasta(\n",
    "    TARA_SAMPLE_ID,\n",
    "    REQUEST_PARAMS\n",
    ")\n",
    "\n",
    "# get_sequences_from_fasta returns a pandas.DataFrame with the extracted sequences\n",
    "print(request_result)"
   ]
  }
 ],
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