Let’s check the “short” way, that is basically a method that avoid the “explosion” of the string. Instead of transforming the sequence from the file from a string to a list, we go and use the string directly, applying one of the methods available to manipulate strings. This time we read the file at once and convert the list to a string using join. To count we simply use the method count on our string. Pretty nice.

#!/usr/bin/env python
#still keep the file fixed
dnafile = "AY162388.seq"
#opening the file, reading the sequence and storing in a list
seqlist = open(dnafile, 'r').readlines()
#let's join the the lines in a temporary string
temp = ''.join(seqlist)
#counting
totalA = temp.count('A')
totalC = temp.count('C')
totalG = temp.count('G')
totalT = temp.count('T')
#printing results
print str(totalA) + ' As found'
print str(totalC) + ' Cs found'
print str(totalG) + ' Gs found'
print str(totalT) + ' Ts found'

That’s the short way: using count. This is a method that when applied on a string counts the number of times the substring appears in our string. We can even set a start and ending point to count. Notice one difference in this script to the previous examples: after we join the items of the list into a string we do not remove the carriage returns. Because in this case we don’t need it, as it will be an extra character there that won’t make any harm.
Download the above code from the repository.