Bioinformatics Programming Classes

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  • Recommended book: Learning Python, Mark Lutz, David Ascher, O'Reilly Media

... after this class ...

If you are thinking of choosing the Bioinformatics profile (even if you're not sure yet) you should already (now) enroll in the course Inleiding programmeren (Python) course ID 401096 via VUnet.

Course Material

Class 1 - intro to linux

Class 2 - python shell: print, operator, types, if exercise: 'calculation' script

Class 3 - lists, for exercise: sum i over n; n!

Class 4 - Functions, scope, namespace, import, while exercise: calculator using functions; interactive calculator with error handling; guessing game

Class 5 - file I/O, dictionaries, string manipulation (e.g., split) exercise: codon table & translation

Class 6 - Regular expressions

* Media:ProgrammingClass6.pdf

Class 7 - Putting everything together exercise: GO parsing


Only the assignments of Class 5 and Class 7 will be graded (the others you may hand in if you want more detailed feedback). We use the following grading scheme for Class 5 asignment:

Item points comments
Runs 2 does it run without (compilation) errors?
Output 2 produces correct output? is output clear/readable?
Flexibility/parameters 1 are different types of input handled correctly? Are parameters and file names not hard-coded?
Strucure/modularity 1 are functions used? locgical function names? no code before/inbetween function declarations?
Readability 2 logical variable names? Consistent indentation?
Efficient 1 is the implementation logical and efficient?
Extensions 3 about 1 point for each of the possible extensions
Total: 12 (if you do all extensions)

and for Class 7 assignment:

Item points comments
Correctness 3
Efficiency 2
Structure / Readability 2 location of main code, no unnecessary global variables, consistent indentation, useful comments, good function and variable names
Robustness / Error-handling 2 useful error messages, check whether files exist, skipping empty strings, check whether number of arguments is correct
Extension(s) 1
Total 10 (includes extension)

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