Most commonly used tools are written in compiled languages like C or java simply because they run faster and the ability to access low level memory resources are crucial to analyzing large amounts of data. When python is used in these packages, it is usually in the form of 'pipeline glue'.
Tophat (http://tophat.cbcb.umd.edu/) is a perfect example of that. It consist of several smaller programs written in C. Python is then used to interpret user paramters and run the smaller programs in sequence.
Interpreted languages like python or perl are usually used for format conversions or statistics reporting.
Good place to start for real examples is to read up on BioPython (http://biopython.org/wiki/Biopython). Their tutorials have tons of real life examples. You can come up with small projects for yourself like writing a script that analyzes gc content of a fasta file, or a script that parses a blast output file and filter on various criteria.
modified 3.0 years ago
3.0 years ago by
Damian Kao ♦ 12k