Module-1_bash-jupyter-git/1.8_find_git_stringreplacement_questions.ipynb

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    "# find\n",
    "\n",
    "Syntax to find all .txt files in a directory,\n",
    "\n",
    "```\n",
    "find ./<dir-name> -name \"*.txt\"\n",
    "```\n",
    "\n",
    "Syntax to execute a command on all the files that match a pattern.\n",
    "\n",
    "```\n",
    "find ./<dir-name> -name \"*.txt\" -exec bash -c 'wc -l $1' _ {} \\;\n",
    "```\n",
    "\n",
    "# Git\n",
    "\n",
    "Git Commands,\n",
    "\n",
    "```\n",
    "cd test-repo/\n",
    "git init # Start a git repository\n",
    "git add . # Adds files into the git index\n",
    "git commit -m \"Message here\" # Takes a snapshot of the index\n",
    "git push <remote-url> master # Pushed commits to a remote repository\n",
    "git pull # Pulls from a remote repository\n",
    "```\n",
    "\n",
    "# String Replacement\n",
    "\n",
    "Command to replace pattern in string,\n",
    "\n",
    "```\n",
    "a=\"helloworld\"\n",
    "a=${a/world/hello}\n",
    "echo $a\n",
    "```\n",
    "\n",
    "# FASTQs\n",
    "\n",
    "Command to extract all read names from FASTQ files,\n",
    "\n",
    "```\n",
    "awk 'NR%4==1' data/tmp/simulated1.R1.fq\n",
    "```\n",
    "\n",
    "## Questions\n",
    "\n",
    "1. Count number of lines in each .txt files in ./data/tmp/ folder.\n",
    "2. Create a local `git` repository on your account. Add atleast two files and make a commit. \n",
    "3. Push these changes to a remote repository and add the url here.\n",
    "4. Print all nucleotide sequences from data/tmp/simulate1.R1.fq\n",
    "\n",
    "## HW\n",
    "\n",
    "1. Count number of characters in the filename of each .txt file in ./data/tmp/ folder.\n",
    "3. Print all nucleotide sequences from ./data/fastq/simulated1.R1.fq by replacing all 'T's in the nucleotide sequences with 'U's. Hint: ${variable//123/112} will replace all occurences of 123 with 112."
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