使用python计算字母在特定位置出现的次数

Question

I'm a python beginner and I've come across this problem and I'm not sure how I'd go about tackling it.

If I have the following sequence/strings:

GATCCG

GTACGC

How to I count the frequency each letter occurs at each position. ie) G occurs at position one twice in the two sequences, A occurs at position 1 zero times etc.

Any help would be appreciated, thank you!

Answer 1

You can use a combination of defaultdict and enumerate like so:

from  collections import defaultdict

sequences = ['GATCCG', 'GTACGC']
d = defaultdict(lambda: defaultdict(int))  # d[char][position] = count
for seq in sequences:
    for i, char in enumerate(seq):  # enum('abc'): [(0,'a'),(1,'b'),(2,'c')]
        d[char][i] += 1

d['C'][3]  # 2
d['C'][4]  # 1
d['C'][5]  # 1

This builds a nested defaultdict that takes the character as first and the position as second key and provides the count of occurrences of said character in said position.

If you want lists of position-counts:

max_len = max(map(len, sequences))
d = defaultdict(lambda: [0]*max_len)  # d[char] = [pos0, pos12, ...]
for seq in sequences:
    for i, char in enumerate(seq): 
        d[char][i] += 1

d['G']  # [2, 0, 0, 0, 1, 1]

Answer 2

Not sure this is the best way but you can use zip to do a sort of transpose on the the strings, producing tuples of the letters in each position, eg:

x = 'GATCCG' 
y = 'GTACGC'

zipped = zip(x,y)

print zipped

will produce as output:

[('G', 'G'), ('A', 'T'), ('T', 'A'), ('C', 'C'), ('C', 'G'), ('G', 'C')]

You can see from the tuples that the first positions of the two strings contain two Gs, the second positions contain an A and a T, etc. Then you could use Counter (or some other method) to get at what you want.