Bioinformatics I WS 2014/14 Assignment 0: start with Python! 1

Prof. Dr. Daniel Huson
Anna Gorska, Rewati Tappu
Zentrum für Bioinformatik
Fachbereich Informatik
Mathematisch-Naturwissenschaftliche Fakultät
Bioinformatics I
Assignment 0: start with Python!
1
WS 2014/14
Due: 22 October 2014
Download & install Python 2.7
not Python 3, since it is not backwards compatible what means majority of packages do not
work:
• in Linux it should be there (type python in the Terminal)
• for all platforms you can use Anaconda
• find you favorite IDE or a text editor (Sublime, Eclipse, Aptana Studio, list of all:
wiki.python.org/moin/IntegratedDevelopmentEnvironments)
2
Explore an interactive shell
• print "Hello, World!"
• try out divisions, e.g. 20/3 and 20.0/3.0, also 20%3
• make Python list the files in your Desktop directory
• write the content of the Desktop directory to a variable
• make a dictionary with the contents of all of the directories you have in your Desktop
directory..
If you like interactive shell you will like iPython even more.
3
Make sure that you know:
• How to construct an if, while, for statements.
• What is the difference between tuple, list and dictionary.
• What is PEP8.
4
Write a simple DNA tool-set (10 points)
• Read DNA sequence from FASTA file. The file you can find on the website:
https://ab.inf.uni-tuebingen.de/teaching/ws14/bioinf, Assignment 0 (1 point).
• Compute and plot GC-content (parameter: window-size) (3 points).
• Compute and plot k-mers histogram (parameter: k-mer length) (3 points).
• Find potential ORFs (1 point).
• Transcribe and translate (2 points).
Make your code easy to read: comments (what does every function do), informative names of
variables/functions, PEP8 formatting.. Don’t forget to label axes!
2