Monday, August 3, 2015

Bioinformatics in Python: GC content


Abstract: calculate GC content with a given DNA sequence

The script:
# -*- coding: utf-8 -*-
"""
Created on Mon Aug  3 14:29:46 2015

@author: yuan
"""


def GC_content(DNA, digits=1):
   
    base_len=float(len(DNA))
    G=DNA.count('G')
    C=DNA.count('C')
    #
    GC_ratio=(G+C)*100/base_len
    #print GC_ratio
    GC_content=round(GC_ratio, digits)
    return GC_content

if __name__=='__main__':
    #GC content
    DNA='TTTTTTGTTTTGAATACGTGTCAACCCCGGCGCTATGCTAGTCTGTAAAAA'

    print 'GC content:', GC_content(DNA, 3)

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