Micropost: Python Scripts with Unix Pipes

It is possible to write a python script that can take standard-in as an input. This is very useful for quick and dirty bioinformatics pipelines. 


Here's an example: Pretend I have a genotype file with chromsomes in the first column, and genotypes in the second column. I would like to find the complement of the genotypes (perhaps to get the data in the opposite orientation). Furthermore, say I am only interested in data that has to do with chromosome 1.


cat genotypefile.txt | awk '{if ($1="chr1"){print $0}}' | python complement.py


This would do it.


The python script (complement.py) would look something like this:


import sys


def reverseBase(base):
        if base == "A":
                return "T"
        elif base == "T":
                return "A"
        elif base == "G":
                return "C"
        elif base == "C":
                return "G"
        else:
                return "N"


def complement(genotype):
        newgeno=''
        for i in genotype:
                newgeno=newgeno+reverseBase(i)
        return newgeno




for i in sys.stdin.readlines():
        line = i.strip('\n').split('\t')
print complement(line[1])


The function names could be better in the example script, but the key is that we loop through "sys.stdin.readlines()". "sys.stdin" allows us to pipe in standard input.