The Unix Shell: Exercises

Exercise 1

List all directories with the string ‘PM’ in the parent directory.

Exercise 2

• Create the folder foo/bar/baz

• Create a file containing ‘Hello world’ named hello.txt in the foo/bar directory

• Delete the foo folder and everything in it, including subdirectoreis.

EXercise 3

• Download an example FASTA file from https://molb7621.github.io/workshop/_downloads/sample.fa
• Download the example FASTQ file from https://molb7621.github.io/workshop/_downloads/SP1.fq

• Show only lines 5-8 from the SP1.fq

• Create an MD5 checksum file MD5SUM for the FASTA and FASTQ files

• Crate a tar gzipped archive called examples.tar.gz that contains these two files

• Delete the FASTA and FASTQ files

• Recover the original files from examples.tar.gz

• Confirm that the MD5 checksums are correct for the recovered files

Exercise 4

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.

Exercise 5

• Write a shell script that will report the number of lines in each file within the current directory.

cat > count_lines.sh << 'EOF'

<Write your script here>

EOF

• Make the file executable

• Run the file