Question

如果之前有人问我，我很抱歉，但我甚至不知道该搜索什么。

我刚刚开始学习python，而我目前正在编写我的第一个程序。这个想法是识别蛋白质序列中的所有开放阅读框架，对于非生物学家来说，这意味着识别所有出现的＆＃34; M ... *＆＃34;在一个字符串中。

这是我到目前为止所做的，它几乎可以正常工作，但每次打印都会重复打印而不是跳到下一个＆＃34; M ...＆＃34;。

# calculates amino acid sequence from nucleotide sequence
protein = nucleotide_seq.transcribe().translate()
print("5'3' Frame 1: \n" + protein)

# Calculates all open reading frames in protein sequence
for n in range(len(protein)):
    met = protein.find("M", n)
    stop = protein.find("*", met)
    orf = protein[met:stop]
    print("Open reading frame starting at residue " + str(met+1) + " : " + orf)
    nextmet = protein.find("M", stop)
    n += nextmet

蛋白质示例：

DIMGYF * GLTGSR * VLSSGWIRAQSCTECG * SSEAGVEVRGVRQTDRHSQPARSAV * SELQILFSFHLLSNCPELAPVAPGLVFRECPESLVSSRPREESPAAQALLTAAESSGTHAPAGGSRRAAAAAKNFPGWEDRRQVAESRSQLLQAFPAS * ASPRR * RPEGGGEPRKRRRTCAQLRSHRLLNLGEREPRLPGAPSP * QRRRGQVVGVRAAKTRRRPATAGSALIRSAGRAAALGSEFACGLRGTAAHEERSVSDRDFSKPGSARESTSKSAGGILINPALPGASW * GGRSGDDSQRVRALLEKLSLSKAPGGAGVPRLPQPCCGPETCARSPN * PHVK * RTVL * LQRWKRPSMTMPSTPRSSRPRADLMATVTPRS *

Answer 1

n += nextmet无法执行您想要的操作，因为当控件返回到for循环的顶部时，n会重置为范围中的下一个数字。因此，您可以使用for循环，而不是使用while循环。例如，

maxloop = len(protein)
n = 0
while n < maxloop:
    met = protein.find("M", n)
    if met == -1:
        break
    #etc 
    n = nextmet + 1

我把if语句放在那里，因为如果find找不到它的目标，它会返回-1。

这是一个更完整的演示，现在您已经为我们提供了一些数据可供使用。

protein = '''DIMGYF*GLTGSR*VLSSGWIRAQSCTECG*SSEAGVEVRGVRQTDRHSQPARSAV*
SELQILFSFHLLSNCPELAPVAPGLVFRECPESLVSSRPREESPAAQALLTAAESSGTHAPAGGSRRAAAAA
KNFPGWEDRRQVAESRSQLLQAFPAS*ASPRR*RPEGGGEPRKRRRTCAQLRSHRLLNLGEREPRLPGAPSP
*QRRRGQVVGVRAAKTRRRPATAGSALIRSAGRAAALGSEFACGLRGTAAHEERSVSDRDFSKPGSARESTS
KSAGGILINPALPGASW*GGRSGDDSQRVRALLEKLSLSKAPGGAGVPRLPQPCCGPETCARSPN*PHVK*
RTVL*LQRWKRPSMTMPSTPRSSRPRADLMATVTPRS*'''

#Get rid of newlines
protein = protein.replace('\n', '')

print("5'3' Frame 1:\n{0}\n".format(protein))

maxloop = len(protein)
n = 0
while n < maxloop:
    met = protein.find("M", n)
    if met == -1:
        break

    stop = protein.find("*", met)
    if stop == -1:
        print('Error: no * found for frame starting at residue', met + 1)
        break

    orf = protein[met:stop]
    print("Open reading frame starting at residue", met + 1, ":", orf)

    n = stop + 1

<强>输出

 5'3' Frame 1:
DIMGYF*GLTGSR*VLSSGWIRAQSCTECG*SSEAGVEVRGVRQTDRHSQPARSAV*SELQILFSFHLLSNCPELAPVAPGLVFRECPESLVSSRPREESPAAQALLTAAESSGTHAPAGGSRRAAAAAKNFPGWEDRRQVAESRSQLLQAFPAS*ASPRR*RPEGGGEPRKRRRTCAQLRSHRLLNLGEREPRLPGAPSP*QRRRGQVVGVRAAKTRRRPATAGSALIRSAGRAAALGSEFACGLRGTAAHEERSVSDRDFSKPGSARESTSKSAGGILINPALPGASW*GGRSGDDSQRVRALLEKLSLSKAPGGAGVPRLPQPCCGPETCARSPN*PHVK*RTVL*LQRWKRPSMTMPSTPRSSRPRADLMATVTPRS*

Open reading frame starting at residue 3 : MGYF
Open reading frame starting at residue 358 : MTMPSTPRSSRPRADLMATVTPRS

Answer 2

import re
protein = "DIMGYF*GLTGSR*VLSSGWIRAQSCTECG*SSEAGVEVRGVRQTDRHSQPARSAV*SELQILFSFHLLSNCPELAPVAPGLVFRECPESLVSSRPREESPAAQALLTAAESSGTHAPAGGSRRAAAAAKNFPGWEDRRQVAESRSQLLQAFPAS*ASPRR*RPEGGGEPRKRRRTCAQLRSHRLLNLGEREPRLPGAPSP*QRRRGQVVGVRAAKTRRRPATAGSALIRSAGRAAALGSEFACGLRGTAAHEERSVSDRDFSKPGSARESTSKSAGGILINPALPGASW*GGRSGDDSQRVRALLEKLSLSKAPGGAGVPRLPQPCCGPETCARSPN*PHVK*RTVL*LQRWKRPSMTMPSTPRSSRPRADLMATVTPRS*"
for match in re.finditer('M([^\*]+)\*', protein):
    print match.start()+1, match.group()



>3 MGYF*
>358 MTMPSTPRSSRPRADLMATVTPRS*

如果M...M..*不是有效结果，您可以将M添加到禁止的字符：M([^\*M]+)\*。

>3 MGYF*
>374 MATVTPRS*

Answer 3

您接收重复的原因是由于您正在使用for循环并将n递增1而不是将n移动到前一帧的末尾：

# Calculates all open reading frames in protein sequence
n = 0
length = len(protein)
while n < length:
    met = protein.find("M", n)
    stop = protein.find("*", met)
    if stop == -1:  # Stop is beyond boundary of protein
        break
    orf = protein[met:stop]
    print("Open reading frame starting at residue " + str(met+1) + " : " + orf)
    n = stop + 1

打印以x开头并以y结尾的字符串中的所有匹配项

3 个答案: