{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "Write_sh_file.ipynb",
      "provenance": []
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "code",
      "source": [
        "#Mount Google Drive\n",
        "from google.colab import drive\n",
        "drive.mount('/content/drive')"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "H1vtyy63ItD9",
        "outputId": "bd8375aa-eb4e-433a-fdbb-b9b4baeebb6d"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Mounted at /content/drive\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "uyqZcyu7Hc2_"
      },
      "outputs": [],
      "source": [
        "#Set range for file names\n",
        "START = 281\n",
        "STOP = 694\n",
        "#Set consistent part of SRR accession number\n",
        "srr_begin = \"SRR8737\"\n",
        "\n",
        "#Open file and begin writing\n",
        "sh_file = open(r\"/content/drive/MyDrive/AMR/File_Loading/fastq_to_contig.sh\", \"w\")\n",
        "sh_file.write(\"#!/usr/bin/bash\\n\\n\")\n",
        "\n",
        "#Create loop for printing commands\n",
        "for i in range(START,STOP):\n",
        "  if (i>535 and i<595 and i!=592 and i!=540):\n",
        "    break\n",
        "  #Set remainder of command to be printed\n",
        "  output_path = \"Contig_FASTQ/%s%s\" %(srr_begin,str(i))\n",
        "  input_path_1 = \"FASTQ/%s%s/%s%s_1.fastq\"%(srr_begin,str(i),srr_begin,str(i))\n",
        "  input_path_2 = \"FASTQ/%s%s/%s%s_2.fastq\"%(srr_begin,str(i),srr_begin,str(i))\n",
        "  final_string = \"python3 /home/ssur/Applications/SPAdes-3.15.4-Linux/bin/spades.py -o %s -1 %s -2 %s\\n\"%(output_path, input_path_1, input_path_2)\n",
        "  sh_file.write(final_string)\n",
        "sh_file.close()"
      ]
    }
  ]
}