如何在Python上使用字典从文件更改值

Question

I'm doing a biology degree and feel like I've been thrown in at the deep end with python, as I've never coded before, and the 'teaching' was pretty much non-existent. Anyway, they've given this file of gene sequences, which pretty much looks like :

En123, ATGCCGAATA

En124, ATGCCAGTAT

but much longer with way more genes. They want it converted into a protein sequence. So far, I've got...

with open('DNA_sequences.csv', 'r') as f:

for line in f:
    columns = line.rstrip("\n").split(",") #remove end of line charcters and split at commas to produce a list
    ensemblID = columns[0] #ensemblID is first element in our list
    gene_sequence = columns [1] #gene_name is second element in list

wasn't sure if I needed the columns or not.

I've also made a dictionary for the protein sequence, with the amino acid and the corresponding codon.

protein_sequence= {'TTT': 'F', 'CTT': 'L', 'GAT':'D'} etc.

So I'm wondering how to I split the gene sequence in my file into codons, then pass it through the dictionary so I get the sequence of amino acid names.

i.e. gene_sequence= TTTCTTTGAT to protein_sequence= FLD

(Sorry for being so incompetent!)

Answer 1

so to load the csv I'd use the csv module like so:

import csv

with open(filepath) as csvFile:
    reader = csv.reader(csvFile)
    data = [row for row in reader]

then to convert the gene sequence:

geneSeq = "TTTCTTTGAT"

acids = [geneSeq[i:i+3] for i in range(0, len(geneSeq), 3)]

proteinSequenceString = ""
for a in acids:
    proteinSequenceString += protein_sequence[a]

Answer 2

You can iterate over gene_sequence in chunks of 3 and lookup codons in your dictionary:

>>> gene_sequence = 'TTTCTTGAT'
>>> protein_sequence = {'TTT': 'F', 'CTT': 'L', 'GAT': 'D'}
>>> ''.join(protein_sequence[gene_sequence[i:i+3]] for i in range(0, len(gene_sequence), 3))
'FLD'