Question

There is a file lets call it the.faa.

It contains all of the polypeptide coding sequences in the E. coli K12 genome in FASTA format.

Your task for this exercise is to generate an amino acid usage report with counts only, and in no particular order. Your output should look like this:

T: 69645

G: 95475

V: 91683

Y: 36836

H: 29255

Answer 1

*** Source Code ***

with open("the.faa") as ecoli: # will close your file automatically

                from collections import defaultdict

                counts = defaultdict(int)

                for line in ecoli: # iterate over file object, no need to read all contents into memory

                                if line.startswith(">"): # skip lines that start with >

                                                continue

                                for char in line: # just iterate over the characters in the line

                                                if char in {"A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y"}:

                                                                counts[char] += 1

                total = float(sum(counts.values()))      

                for key,val in counts.items():

                                print("{}: {}".format(key,val))    

*** Output ***              

(Note : Test it with yout the.faa file. Mine is for testing)

L: 2540 Y: 657 T 1222 K: 1048 : 1295 : 881 I: 1447 E: 1443 H 568 P: 1084 P:1001 W: 386 M: 722 S: 1248 G: 1904 A: 2424 V: 1686 R: 1360 C: 328 : 1057