DNA-蛋白翻译过程的Python实现

引言

最近为了给平台上加上一个将DNA序列翻译为蛋白序列的工具，写了一个任何生信玩家初学时都会写的代码。看了一些别人的翻译工具，我也想尽量把代码写的完整一点，在这个过程中首次接触并使用了BioPython，目前看起来还是很好用的。

代码

#!/bin/python3

from Bio.Seq import translate, reverse_complement
from Bio import SeqIO
from Bio.SeqIO.FastaIO import SimpleFastaParser
import os
import sys
import getopt
import warnings
import time

warnings.filterwarnings("ignore")

def translate2(input_file, translated_file, corr_nucl_file, corr_prot_file, summary_file, read_start, rev_comp, no_stop, genetic_code):
	'''
	input_file: nucleic acid sequence fasta file
	translated_file: output file 1, protein sequence fasta file
	summary_file: input file information
	read_start: 1(default). The position that translation starts
	rev_comp: no(default). Do not use reverse complemetary sequences for translation.
	non_stop: yes(default). Show stop codon as * in translated sequence.
	'''
	#Translate
	nucl_dict = SeqIO.to_dict(SeqIO.parse(input_file,"fasta"), key_function = lambda rec: rec.description) #keep whitespace in FASTA header
	prot_dict = {
   }
	corr_nucl_dict = {
   }
	corr_prot_dict = {
   }

	read_start = int(read_start)
	stop_sign = 0 #count how many sequences contain stop codon
	for key in nucl_dict:
		nucl_seq = nucl_dict[key].seq[read_start-1:]
		if rev_comp == 'no':
			prot_seq = translate(nucl_seq,table=genetic_code)
		else:
			prot_seq = translate(reverse_complement(nucl_seq),table=genetic_code)
		prot_dict[key] = prot_seq
		if '*' in prot_seq:
			stop_sign