{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# The Unix Shell: Exercises"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Exercise 1**\n",
    "\n",
    "List all directories with the string 'PM' in the **parent** directory."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Exercise 2**\n",
    "\n",
    "- Create the folder `foo/bar/baz`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- Create a file containing 'Hello world' named hello.txt in the `foo/bar` directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- Delete the `foo` folder and everything in it, including subdirectoreis."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**EXercise 3**\n",
    "\n",
    "- Download an example FASTA file from https://molb7621.github.io/workshop/_downloads/sample.fa\n",
    "- Download the example FASTQ file from https://molb7621.github.io/workshop/_downloads/SP1.fq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- Show only lines 5-8 from the SP1.fq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- Create an MD5 checksum file MD5SUM for the FASTA and FASTQ files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- Crate a tar gzipped archive called `examples.tar.gz` that contains these two files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- Delete the FASTA and FASTQ files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- Recover the original files from `examples.tar.gz` "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- Confirm that the MD5 checksums are correct for the recovered files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Exercise 4**\n",
    "\n",
    "Find any file(s) with the string `GATCGTACGTACGTA` and the line number on which it occurs within files that have the `.fa` or `.fq` extensions within the current directory."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Exercise 5**\n",
    "\n",
    "- Write a shell script that will report the number of lines in each file within the current directory. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "cat > count_lines.sh << 'EOF'\n",
    "\n",
    "<Write your script here>\n",
    "\n",
    "EOF"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- Make the file executable"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- Run the file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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  "kernelspec": {
   "display_name": "Bash",
   "language": "bash",
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   "file_extension": ".sh",
   "mimetype": "text/x-sh",
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}