Python Storing & Printing Data from a text file

Question

I'm trying a Python script that takes from the user a sequence of certain letters, (A, C,G ,T) and prints the percentage of A's, C's, G's, and T's.

For example if the user types AGGTGACCCT then the output should be A: 20 C: 30 G: 30 T: 20

I'm fairly experienced with Java, but new to Python. I don't how to use Scanners like I would in Java. I tried searching through a reference library but couldn't really figure anything out.

Answer 1

collections.Counter is a very handy tool and worth learning about when you start using python.

from collections import Counter

inp = input("Enter letters") # input() if using python 3

l = len(inp.strip()) # get length of input string ,inp.strip() removes any whitespace, just use len(inp) if you want to include

c = Counter(inp)

for char in c:
    c[char] = c[char] * 100 / l  # don't need to cast as float for python 3
print (c)
Counter({'C': 30.0, 'G': 30.0, 'A': 20.0, 'T': 20.0})

There is a module csv that has a DictWriter that will be able to write the data to file.

Answer 2

You can read directly from the standard input stream, sys.stdin , like so:

$ cat read.py 
import sys

userin = sys.stdin.read()
print [c for c in userin]

$ python read.py 
HELLO
['H', 'E', 'L', 'L', 'O', '\n']

And then you can pipe a text file to stdin, like:

$ cat input.txt 
HELLO
$ python read.py < input.txt 
['H', 'E', 'L', 'L', 'O', '\n']

Or, if you want to read a file directly:

>>> import io
>>> with io.open('input.txt', mode='rb') as f:
...     print [c for c in f.read()]
... 
['H', 'E', 'L', 'L', 'O', '\n']

Answer 3

If you can save the sequence in a comma separated file (csv), then you could do something along the lines of:

import pandas as pd

sequence = pd.read_csv(file_name)
As = 0
Cs = 0
Gs = 0
Ts = 0
total = len(sequence)

for letter in sequence:
    if letter == 'A':
        As += 1.0
    elif letter == 'C':
        Cs += 1.0
    elif letter == 'G':
        Gs += 1.0
    elif letter == 'T':
        Ts += 1.0

percent_A = As/total
percent_C = As/total
percent_T = As/total
percent_G = As/total

Or:

import pandas as pd

sequence_list = []
sequence = pd.read_csv(file_name)
for letter in sequence:
    sequence_list.append(letter)

As = sequence_list.count('A')
Cs = sequence_list.count('C')
Gs = sequence_list.count('G')
Ts = sequence_list.count('T')

total = len(sequence_list)

percent_A = As/total
percent_C = As/total
percent_T = As/total
percent_G = As/total

This general structure holds for tsvs as well.