Calculates the GC content across all sequences in an input fasta file

gc_content.py

#!/usr/bin/env python

from sys import argv

from skbio.parse.sequences.fasta import parse_fasta

def calculate_gc_content(input_fasta):
    gc = 0
    total_length = 0

    for _, seq in parse_fasta(input_fasta):
        seq = seq.lower()
        total_length += len(seq)
        gc += seq.count('g')
        gc += seq.count('c')

    return 1.0 * gc / total_length

if __name__ == '__main__':
    with open(argv[1], 'U') as input_fasta:
        gc_content = calculate_gc_content(input_fasta)

    print 'The total fraction of G/C in the input FASTA file is:', gc_content
    print 'Note that this calculation not take into account degeneracies.'