创建通过字典翻译DNA序列的功能

Question

I have a codon table like such

codon = {'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
    'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
    'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
    'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
    'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',
    'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
    'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',
    'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
    'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',
    'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
    'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
    'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
    'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',
    'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
    'TAC':'Y', 'TAT':'Y', 'TAA':'stop', 'TAG':'stop',
    'TGC':'C', 'TGT':'C', 'TGA':'stop', 'TGG':'W'}

I have a fasta file with different sequences like such

CAAAAGCAGGGGATAATTAAATCAACCAAAATGGAAGCAAAACTGCTCGTGTTATTTTGTGCCTTCACCG
CACTGAAAGCTGACACCATTTGTGTGGGCTACCATGCTAACAATTCCACAGACACTGTCGACACAATACT
AAAGCAGGGGATAATTAAATCAACCAAAATGGAAGCAAAACTGCTCGTGTTATTTTGTGCCTTCACCGCA
CTGAAAGCTGACACCATTTGTGTGGGCTACCATGCTAACAATTCCACAGACACTGTCGACACAATACTGG

I want to parse the file so that the three nucleotides are outputting a protein. For example CAA should output Q. This is what I have so far

fasta = open('Fasta.txt', 'r')

def readSeq(fasta):
    for line in fasta:
        if line.startswith('>'):
            continue
        line = line.strip()
        print(line)

readSeq(fasta)

Answer 1

You should look into implementing a custom stream using Python generator feature. More details are here

Here is the example code:

First you need to change your read seq function to yield one 3 base pair chunk at the time

def readSeq(fasta):
  for line in fasta:
    if line.startswith('>'):
        continue
    line = line.strip()
    chunks = [ line[i*3:i*3+3] for i in range(0, int(len(line)/3)) ]

    yield from chunks

Then you can just iterate over the resulting stream:

fasta = open('Fasta.txt', 'r')
stream = readSeq(fasta)
for seq in stream:
    print (codon[seq])

And you will get output like this:

QKQGIIKSTKMEAKLLVLFCA FTH stop