Introduction to Unix
Solve these assignments in a terminal window, and perhaps using a browser.
- Figure out what the following Unix commands do. You should feel familiar will all of these:
- Create a directory structure for this course in your home directory using
cd. There should be a directory for the course, and within it a directory for each assignment.
- Use the
mancommand to figure out…
- … what the command “ls -l” does.
- … how you delete a directory and its contents with
- Download our GPCR data file (with data concerning G-protein coupled receptors from a number of species) into your course directory and apply the commands from question 1 to answer the following questions. Note: this is about practicing working on the command line!
- How many columns are there (if you count by eye)?
- How many lines is there in the file?
wcto find out how many human GPCRs there are listed. Use techniques from Chapter 5! Do you search for “human” or “Homo sapiens”?
- How long is the shortest sequence listed in the same file? Use
- How many species are named in gpcr.tab?
- Download and extract a directory with Fasta files, that contains 88 Fasta files. Write a shell script that applies a multi alignment software like Muscle or MAFFT (install as necessary!) on each gene family in the directory.
Please have code and answers ready before the Stockholm visit. We will discuss and evaluate your solutions in groups.