demo1.py

#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Thu Sep 14 13:13:04 2017

@author: weishen
"""
#This script cacluates the GC content

#open the file and store it in the variable fh
fh=open("/Users/weishen/Documents/Courses/EEB5300/demo.fasta","r")
#store lines from fh into list called lines
lines=fh.readlines()

NumGenes=0
for l in lines:
     #print l
     if l[0] == ">":
         NumGenes=NumGenes+1
        
print NumGenes

nucleotides=0
countA=0
countG=0
countC=0
countT=0
for l in lines:
    if l[0] != ">":
        for nuc in l:
            if nuc=="A":
                countA=countA+1
                nucleotides=nucleotides+1
            elif nuc=="G":
                countG=countG+1
                nucleotides=nucleotides+1
            elif nuc=="C":
                countC=countC+1
                nucleotides=nucleotides+1
            elif nuc=="T":
                countT=countT+1
                nucleotides=nucleotides+1
            else:
                print "it is a new line character"
print "A:", countA
print "G:", countG
print "T:", countC
print "C:", countT
print nucleotides
print countA+countG+countC+countT

GC=(countG+countC)/float(nucleotides)
print GC