Beginning Python for Bioinformatics

This time we check another functional programming function from Python: filter. As the name implies, filter returns items from a sequence (list, string, etc) that are true to a certain condition defined by the function. The syntax is very similar to map

filter (function, sequence)

and as map it returns a list (except when the sequence is a string or tuple). In the example here we will use lambda to define a one-line function. Let’s say we want to quickly find the sequences that contain a motif, sequences that are stored in a FASTA file (again, this is a very simple example, just a primer). Of course we can use another method, but this time we want to use a functional programming approach. filter suits us best here. Again we will reuse the newly created function that returns only the sequences from a FASTA file and we end up with a script that looks like this

#! /usr/bin/env python

import fasta
import sys

sequences = fasta.read_seqs(open(sys.argv[1], 'r').readlines())
motif = sys.argv[2]

print filter(lambda x:x.find(motif) >= 0, sequences)

We skip the part we already seen and check the last line. Basically each item from the list (sequences) is a string and we are applying the find method in order to find a motif on a position larger or equal to 0. Notice again, the syntax similar to map.

Of course this is not very useful as it is, so next time we will change this script to make it more meaningful.