Wrote a batch processing front-end to REP that uses the annotated P. falciparum strain 3D7 as its test data source from PlasmoDB and processes the results. The program is written using Python and the Biopython library. The Python Regular Expression tutorial and the Python course in Bioinformatics provided essential information along the way. To ensure correctness, the results were compared against a PlasmoDB gene query for the Pfam domain.

In Biopython, processing FASTA file formats are almost trivial:

it = Bio.Fasta.Iterator(handle,
     Bio.Fasta.SequenceParser())

seq = it.next()
while seq:
    print seq.description
    print seq.seq
    seq = it.next()

The comp.lang.python newsgroup is also very helpful. And to close, here are some useful resources available online for Python and Biopython:

• Python Tutorial and Python Library Reference by Guido van Rossum.
• How to Think Like a Computer Scientist: Learning with Python by Allen Downey, for beginners.
• Dive Into Python by Mark Pilgrim, for experienced programmers.