使用Python将其分离成mRNA可读区域以获得分离的蛋白质

Question

我正在尝试创建一个程序来执行以下操作：

• 输入可以是DNA序列(反义或有义(或mRNA序列
• 通过DNA序列，获得互补的信使核糖核酸序列

该程序将寻找并打印mRNA序列的可读区域，并将这些区域翻译成氨基酸序列。

问题是我忘记了分离可读区域，因此可读区域都在一起，AA序列也是如此。将它们分开并呈现结果的最佳方式是什么？

#DNA->RNA->Protein
print ('Are you using a DNA ou RNA string?')
RNAS= 'RNA'
Resp=input().upper()
if "DNA" in Resp: #convert DNA to RNA
print('Is the strand sense or antisense? Meaning, from 5 to 3 or from 3 to 5?')
Resp2= input().upper()
if "ANTISENSE" in Resp2: #reverse
print ('Please input the string')
DNAs=input().upper()
RNAs = DNAs.replace('A', 'u').replace('T', 'a').replace('C', 'g').replace('G', 'c').upper()[::-1]
print ('The complementar RNA strand is:')
print (RNAs)
else:
print ('Please input the string')
DNAs=input().upper()
RNAs = DNAs.replace('A', 'u').replace('T', 'a').replace('C', 'g').replace('G', 'c').upper()
print ('The complementar RNA strand is:')
print (RNAs)
if "RNA" in Resp:
print ('Please input the string')
RNAs=input().upper()
# search for readable regions
def readable(seq, n):
for i in range(0, len(seq), n):
yield seq[i:i+n]
def method(seq, start=['AUG'], stop=['UAA','UAG','UGA']):
response = ''
started = False
for x in readable(seq, 3):
if x in start:
started = True
if x in stop:
started=False
if started:
response += x

yield response
for result in method(RNAs):
b=result
print (' ')
print ('The readable part of the RNA is:')
print(result)
def translate(seq): #translate the readable region

table = {
'AUA':'I', 'AUC':'I', 'AUU':'I', 'AUG':'M',
'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACU':'T',
'AAC':'N', 'AAU':'N', 'AAA':'K', 'AAG':'K',
'AGC':'S', 'AGU':'S', 'AGA':'R', 'AGG':'R',                 
'CUA':'L', 'CUC':'L', 'CUG':'L', 'CUU':'L',
'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCU':'P',
'CAC':'H', 'CAU':'H', 'CAA':'Q', 'CAG':'Q',
'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGU':'R',
'GUA':'V', 'GUC':'V', 'GUG':'V', 'GUU':'V',
'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCU':'A',
'GAC':'D', 'GAU':'D', 'GAA':'E', 'GAG':'E',
'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGU':'G',
'UCA':'S', 'UCC':'S', 'UCG':'S', 'UCU':'S',
'UUC':'F', 'UUU':'F', 'UUA':'L', 'UUG':'L',
'UAC':'Y', 'UAU':'Y', 'UGG':'W', 'UGU':'C',
'UGC':'C'}
protein =""
if len(b)%3 == 0:

for i in range(0, len(seq), 3):
codon = seq[i:i + 3]
protein+= table[codon]
return protein
p = translate(b)
print (' ')
print ('The aa sequence is:')
print (p)
print('')
print('')
print ('Ready to close programm? Yes or no')
Close=input().lower
if "yes" in Close:
print('Bye')

编辑：

def method(seq, start=['AUG'], stop=['UAA','UAG','UGA']):
response = ''
started = False
for x in readable(seq, 3):
if x in start:
started = True
response += ' '
if x in stop:
started=False
if started:
response += x

yield response
for result in method(RNAs):
b=result
print (' ')
print ('The readable part of the RNA is:')
print(result)
print (' ')
print ('Considering a minimum of 30 nucleotides, the readable part of the RNA is:')
f=result.split()
readable_regions=[x for x in f if len(x)>=int(30)] #readable regions

Answer 1

仅修复了初始问题，尚未进行优化更改。

print ('Are you using a DNA ou RNA string?')
RNAS= 'RNA'
Resp=input().upper()
if "DNA" in Resp: #convert DNA to RNA
print('Is the strand sense or antisense? Meaning, from 5 to 3 or from 3 to 5?')
Resp2= input().upper()
if "ANTISENSE" in Resp2: #reverse
print ('Please input the string')
DNAs=input().upper()
RNAs = DNAs.replace('A', 'u').replace('T', 'a').replace('C', 'g').replace('G', 'c').upper()[::-1]
print (' ')
print ('The complementar RNA strand is:')
print (RNAs)
else:
print ('Please input the string')
DNAs=input().upper()
RNAs = DNAs.replace('A', 'u').replace('T', 'a').replace('C', 'g').replace('G', 'c').upper()
print (' ')
print ('The complementar RNA strand is:')
print (RNAs)
if "RNA" in Resp:
print ('Please input the string')
RNAs=input().upper()
# search for readable regions
def readable(seq, n):
for i in range(0, len(seq), n):
yield seq[i:i+n]
def method(seq, start=['AUG'], stop=['UAA','UAG','UGA']):
response = ''
started = False
for x in readable(seq, 3):
if x in start:
started = True
response += '   '
if x in stop:
started=False
if started:
response += x

yield response
for result in method(RNAs):
b=result
print (' ')
print ('The readable part of the RNA is:')
print(result)
print (' ')
print ('Considering a minimum of 30 nucleotides, the readable part of the RNA is:')
f=result.split()
readable_regionslist=[x for x in f if len(x)>=int(30)] #readable regions
separator = '   '
readable_regions=(separator.join(readable_regionslist))
print(readable_regions)

def translate(seq): #translate the readable regions
table = {
'AUA':'I', 'AUC':'I', 'AUU':'I', 'AUG':'M',
'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACU':'T',
'AAC':'N', 'AAU':'N', 'AAA':'K', 'AAG':'K',
'AGC':'S', 'AGU':'S', 'AGA':'R', 'AGG':'R',                 
'CUA':'L', 'CUC':'L', 'CUG':'L', 'CUU':'L',
'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCU':'P',
'CAC':'H', 'CAU':'H', 'CAA':'Q', 'CAG':'Q',
'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGU':'R',
'GUA':'V', 'GUC':'V', 'GUG':'V', 'GUU':'V',
'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCU':'A',
'GAC':'D', 'GAU':'D', 'GAA':'E', 'GAG':'E',
'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGU':'G',
'UCA':'S', 'UCC':'S', 'UCG':'S', 'UCU':'S',
'UUC':'F', 'UUU':'F', 'UUA':'L', 'UUG':'L',
'UAC':'Y', 'UAU':'Y', 'UGG':'W', 'UGU':'C',
'UGC':'C', '   ':'   '}
protein =""
if len(b)%3 == 0:

for i in range(0, len(seq), 3):
codon = seq[i:i + 3]
protein+= table[codon]
return protein
p = translate(b)

p = translate(readable_regions)
print (' ')
print ('The aa sequence is:')
print (p)