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Introduction to the Command Line for Genomic

Date

Instructor

Helper

Website https://datacarpentry.org/shell-genomics

Timings - EDIT FOR YOUR WORKSHOP

Here’s a tentative schedule for the workshop

• Introducing the Shell 09:30-10:00 (30 mins)
• Navigating Files and Directories 10:00-10:50 (50 mins)
• Break 10:50-11:05 (15 mins)
• Working with Files and Directories 11:05-11:50 (45 mins)
• Redirection 11:50-12:35 (45 mins)
• Break 12:35-13:30 (55 mins)
• Writing Scripts and Working with Data 13:30-14:10 (40 mins)
• Project Organization 14:10-14:40 (30 mins)
• Wrap up and feedback 14:40-14:55 (15 mins)

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Introducing the Shell

Exercise:

Use the -l option for the ls command to display more information for each item in the directory.

What is one piece of additional information this long format gives you that you don’t see with the bare ls command? - - -

Navigating Files and Directories

Exercise: FINDING HIDDEN DIRECTORIES

First navigate to the shell_data directory. There is a hidden directory within this directory. Explore the options for ls to find out how to see hidden directories. List the contents of the directory and identify the name of the text file in that directory.

Hint: hidden files and folders in Unix start with ., for example .my_hidden_directory

Exercise: NAVIGATING PRACTICE

Navigate to your home directory. From there, list the contents of the untrimmed_fastq directory.

Exercise: RELATIVE PATH RESOLUTION

Using the filesystem diagram on the lesson page below, if pwd displays /Users/thing, what will ls ../backup display?

Put a + next to the answer you think is correct.

1. ../backup: No such file or directory
2. 2012-12-01 2013-01-08 2013-01-27
3. 2012-12-01/ 2013-01-08/ 2013-01-27/
4. original pnas_final pnas_sub

Working with Files and Directories

Exercise:

Do each of the following tasks from your current directory using a single ls command for each:

1. List all of the files in /usr/bin that start with the letter ‘c’.
2. List all of the files in /usr/bin that contain the letter ‘a’.
3. List all of the files in /usr/bin that end with the letter ‘o’.

Bonus: List all of the files in /usr/bin that contain the letter ‘a’ or the letter ‘c’.

**	Hi	nt:** The bonus question requires a Unix wildcard that we haven’t talked about yet. Try searching the internet for information about Unix wildcards to find what you need to solve the bonus problem.
##	#	Exercise: echo and wildcards

echo is a built-in shell command that writes its arguments, like a line of text to standard output. The echo command can also be used with pattern matching characters, such as wildcard characters. Here we will use the echo command to see how the wildcard character is interpreted by the shell.

BASH

$ echo *.fastq

What would the output look like if the wildcard could not be matched?

Compare the outputs of

1. echo *.missing

2. `l	s	*.missing`
   ##	#	Exercise: command history

Find the line number in your history for the command that listed all the .sh files in /usr/bin. Rerun that command.

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Exercise: Examining Files

1. Print out the contents of the ~/shell_data/untrimmed_fastq/SRR097977.fastq file. What is the last line of the file?

2. From your home directory, and without changing directories, use one short command to print the contents of all of the files in the ~/shell_data/untrimmed_fastq directory.

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Exercise: Examining Files

Use less on the file SRR097977.fastq and find the next three nucleotides (characters) after the first instance of the sequence TTTTT?

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Exercise:

Starting in the shell_data/untrimmed_fastq/ directory, do the following:

1. Make sure that you have deleted your backup directory and all files it contains.
2. Create a backup of each of your FASTQ files using cp. (Note: You’ll need to do this individually for each of the two FASTQ files. We haven’t learned yet how to do this with a wildcard.)
3. Use a wildcard to move all of your backup files to a new backup directory.
4. Change the permissions on all of your backup files to be write-protected.

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Redirection

EXERCISE:

1. Search for the sequence GNATNACCACTTCC in theSRR098026.fastq` file. Have your search return all matching lines and the name (or identifier) for each sequence that contains a match.

2. Search for the sequence AAGTT in both FASTQ files. Have your search return all matching lines and the name (or identifier) for each sequence that contains a match. - - -

EXERCISE

How many sequences are there in SRR098026.fastq? Remember that every sequence is formed by four lines.

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EXERCISE

How many sequences in SRR098026.fastq contain at least 3 consecutive Ns?

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EXERCISE

Print the file prefix of all of the .txt files in our current directory.

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EXERCISE

Remove _2019 from all of the .txt files.

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Writing Scripts and Working with Data

EXERCISE

Open README.txt, add the date to the top of the file, and then save it.

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EXERCISE

We want the script to tell us when it’s done.

Open bad-reads-script.sh and add the line echo "Script finished!" after the grep command and save the file. Run the updated script.

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Project Organization

EXERCISE

Use the mkdir command to make the following directories:

dc_workshop
dc_workshop/docs
dc_workshop/data
dc_workshop/results

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EXERCISE

Using your knowledge of the shell, use the append redirect >> to create a file called dc_workshop_log_XXXX_XX_XX.sh (Use the four-digit year, two-digit month, and two digit day, e.g. dc_workshop_log_2017_10_27.sh)

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