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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# `bash` practicals\n",
+    "\n",
+    "## Directory and file structure\n",
+    "\n",
+    "Using one command move to your home directory."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cd"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Change your directory on your local drive (mounted from virtualbox). "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Confirm that you are in the correct location."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/home/malay\n"
+     ]
+    }
+   ],
+   "source": [
+    "pwd"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Download the data required for the class. The files are `split` into two part because of GitHub limitation."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wget https://github.com/cb2edu/CB2-101-BioComp/raw/2020/01-Linux_101/data/linux_data.tar.xz.partaa\n",
+    "wget https://github.com/cb2edu/CB2-101-BioComp/raw/2020/01-Linux_101/data/linux_data.tar.xz.partab"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Check that there are two files in the directory."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ls"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Join the parts."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cat linux_data.tar.xz.parta* > linux_data.tar.xz\n",
+    "ls"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We don't need the parts anymore."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rm linux_data.tar.xz.parta*"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Unzip the data."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tar -xvJf linux_data.tar.xz"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Using one command list the contents of the reference_data directory that is within the linux_data directory."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Create a new folder in `linux_data` called `selected_fastq`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Copy over the Irrel_kd_2.subset.fq and Mov10_oe_2.subset.fq from raw_fastq to the linux_lesson/selected_fastq folder"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Rename the `selected_fastq`folder and call it `exercise1`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Wildcards"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Do each of the following using a single ls command without navigating to a different directory.\n",
+    "\n",
+    "1. List all of the files in /bin that start with the letter 'c'\n",
+    "2. List all of the files in /bin that contain the letter 'a'\n",
+    "3. List all of the files in /bin that end with the letter 'o'\n",
+    "4. BONUS: Using one command to list all of the files in /bin that contain either 'a' or 'c'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## History\n",
+    "\n",
+    "1. Checking the output of the history command, how many commands have you typed in so far?\n",
+    "2. Use the up arrow key to check the command you used before history command. What is it? Does it make sense?\n",
+    "3. Type several random characters on the command prompt. Can you bring the cursor to the start with Ctrl + A? Next, can you bring the cursor to the end with Ctrl + E? Finally, what happens when you use Ctrl + C?\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Files\n",
+    "\n",
+    "**Do the following in the terminal**\n",
+    "\n",
+    "1. Change directories into genomics_data. You can do this using a full or relative path.\n",
+    "2. Use the less command to open up the file Encode-hesc-Nanog.bed.\n",
+    "3. Search for the string chr11; you'll see all instances in the file highlighted.\n",
+    "4. Staying in the less buffer, use the shortcut to get to the end of the file. \n",
+    "5. Exit the less buffer and come back to the command prompt.\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Searching files\n",
+    "\n",
+    "1. Using `find` command search for the sequence file `Mov10_oe_1.subset.fq`.\n",
+    "2. Search for the sequence CTCAATGAGCCA in Mov10_oe_1.subset.fq. How many sequences do you find?\n",
+    "3. If you want to search for that sequence in **all** Mov10 replicate fastq files, what command would you use?\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Searching and redirection\n",
+    "\n",
+    "How many unique exons are present on chromosome 1 using chr1-hg19_genes.gtf?\n",
+    "\n",
+    "1. Extract only the genomic coordinates of exon features\n",
+    "2. Subset dataset to only keep genomic coordinates\n",
+    "3. Remove duplicate exons\n",
+    "4. Count the total number of exons"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Shell scripts\n",
+    "\n",
+    "1. Write a script `listing.sh`. Add the command which prints to screen the contents of the file `Mov10_rnaseq_metadata.txt`.\n",
+    "2. Add an echo statement for the command, which tells the user \"This is information about the files in our dataset:\"\n",
+    "3. Run the new script. Report the contents of the new script and the output you got after running it."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    " ## Bash variables\n",
+    "\n",
+    "1. Use the `$file` variable as input to the head and tail commands, and modify the arguments to display only four lines from any file. \n",
+    "2. Create a new variable called meta and assign it the value Mov10_rnaseq_metadata.txt. For the following questions, use the $meta variable but do not change directories. Provide the code you would run to:\n",
+    "   \n",
+    "    a. Display the contents of the file using cat.\n",
+    "    b. Retrieve only the lines which contain normal samples. (Hint: use grep)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "    \n",
+    "## Filename\n",
+    "\n",
+    "1. How would you modify basename command above to only return Mov10_oe_1 from the filename `Mov10_oe_1.subset.fq`?\n",
+    "2. Use basename with the file Irrel_kd_1.subset.fq as input. Return only Irrel_kd_1 to the terminal."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## `for` loop\n",
+    "\n",
+    "Write a loop to print out the number of lines in each fasta file in the dataset. The output should look something like this:\n",
+    "```\n",
+    "  Irrel_kd_1.subset.fq 891684\n",
+    "  Irrel_kd_2.subset.fq 767072\n",
+    "  Irrel_kd_3.subset.fq 586196\n",
+    "  Mov10_oe_1.subset.fq 1223600\n",
+    "  Mov10_oe_2.subset.fq 1110016\n",
+    "  Mov10_oe_3.subset.fq 690816\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Bash",
+   "language": "bash",
+   "name": "bash"
+  },
+  "language_info": {
+   "codemirror_mode": "shell",
+   "file_extension": ".sh",
+   "mimetype": "text/x-sh",
+   "name": "bash"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}