Lesson 9: Perl Subroutines

or
Learning Perl, ed. 5:
Chapter 4; p. 55-67

or
Learning Perl, ed. 6:
Chapter 4; p. 63-71

Subjects covered

• Subroutines: a subroutine is both a way of hiding complexity and a way of reusing code.
• Scope of variables.

Necessary files to complete this exercise
To download the files to your system, just press the Shift key while you left click on the blue link. Follow the instructions.
dna7.fsa
ex5.acc
dna-array.dat

All the following exercises have to be done in Perl

1. Make a subroutine that take a DNA sequence (string) as parameter and return the complement strand (reverse complement). Use it to improve 7.3 which works on dna7.fsa.
2. Improve on 2.10 by making a subroutine that calculates the factorial. Add some input control (make sure you get positive integers, when you ask for a number).
3. Make a subroutine, that returns the relevant one-letter designation for the correct ammino acid, when you give it a codon (3 bases). You can find a list here. If something invalid is given as input to the subroutine, return an error code (make one up). You can reuse the hash from last lesson for most of the exercise, if you want.
4. Make a subroutine that (only) removes duplicates from a list and returns the clean list. Use it to improve 6.3.
5. You do not need to use subroutines in this exercise. Study the file DNA-array.dat a bit. This is real DNA array data taken from a number of persons, some controls and some suffering from colon cancer. If you look at the second line there is a lot of 0 and 1. A '0' means that values in that column are from a cancer patient and a '1' means data are from a control (healty person). The data are all log(intensity), i.e. the logarithm of the mesured intensity of the relevant spot on the dna-chip. The data in this file will be used in comming exercises. Oh, yes - the data/columns are tab separated. The second item on each line is the accession number for that particular gene.
   Now make a program that extracts data from dna-array.dat. It shall ask for an accession number (unless you have given it on the command line). Make sure your program handles both situations. Then it shall search in the file for the data concerning that accession number. If it does not find it (you gave a wrong accession no), complain and stop. Otherwise it shall display the data in two tab separated columns. First column shall be the data from the cancer patients, second column for the controls. And yes, there are not the same number of sick and healthy people - be able to handle that.