Question

尝试让dna阅读脚本正常工作，现在只是部分。这需要一串'A'，'T'，'C'或'G'字符，并根据子串是以'ATG'开头并以'TAA'，'TGA'，'TAG'结尾来查找基因。 printAllGenes（）在找到的每一行的新行上打印出一个dna链（已识别的子串），并继续通过输入字符串，直到找不到更多内容。由于findStopCodon（）的else子句中的错误，printAllGenes（）似乎无法完成执行。

gene_sequence = 'AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTCACCCTTCTAACTGGACTCTGACCCTGATTGTTGAGGGCTGCAAAGAGGAAGAATTTTATTTACCGTCGCTGTGGCCCCGAGTTGTCCCAAAGCGAGGTAATGCCCGCAAGGTCTGTGCTGATCAGGACGCAGCTCTGCCTTCGGGGTGCCCCTGGACTGCCCGCCCGCCCGGGTCTGTGCTGAGGAGAACGCTGCTCCGCCTCCGCGGTACTCCGGACATATGTGCAGAGAAGAACGCAGCTGCGCCCTCGCCATGCTCTGCGAGTCTCTGCTGATGAGAACACAGCTTCACTTTCGCAAAGGCGCAGCGCCGGCGCAGGCGCGGAGGGGCGCGCAGCGCCGGCGCAGGCGCGGAGGGGCGCGCCCGAACCCGAACCCTAATGCCGTCATAAGAGCCCTAGGGAGACCTTAGGGAACAAGCATTAAACTGACACTCGATTCTGTAGCCGGCTCTGCCAAGAGACATGGCGTTGCGGTGATATGAGGGCAGGGGTCATGGAAGAAAGCCTTCTGGTTTTAGACCCACAGGAAGATCTGTGACGCGCTCTTGGGTAGAGCACACGTTGCTGGGCGTGCGCTTGAAAAGAGCCTAAGAAGAGGGGGCGTCTGGAAGGAACCGCAACGCCAAGGGAGGGTGTCCAGCCTTCCCGCTTCAACACCTGGACACATTCTGGAAAGTTTCCTAAGAAAGCCAGAAAAATAATTTAAAAAAAAATCCAGAGGCCAGACGGGCTAATGGGGCTTTACTGCGACTATCTGGCTTAATCCTCCAAACAACCTTGCCATACCAGCCCATCAGTCCTCTGAGACAGGTGAAGAACCTGAGGTCGCAGGAGGACACCCAGAAGGTCCAGAGAGAGCCTCCTAGGCCCCCCACCTCCCCCCGTGGCAGCTCCAACCCCAGCTTTTTCACTAGTAAGGCAGTCGGGCCCCTGGGCCACGCCCACTCCCCCAAGCGGGGAAGGAGCTTCGCGCTGCCGCTTGGCTGGGGACTGGGCACCGCCCTCCCGCGGCTCCTGAGCCGGCTGCCACCAGGGGGCGCGCCAGCGGTGTCCGGGAGCCTAGCGGCGCGTGTGCAGCGGCCAGTGCACCTGCTCTGGCCCTCGCCGCGGTCTCTGCCAGGACCCCGACGCCCAGCCTGACCCTGCCATTCAGCGGGGCTGCGGCTCCACGGCCTGCGACAGCAGCCCCACCTGGCATTCAGCGCGCTCCCGGGGGCAGAGGTCGCGGTGTCCTCACGCTGTGGTGCCGGCCTACAACCCCCACGCCGGGCTCGGGCCCGGCGGAGGAGGGCGATGCTCCCCGGGTAGGACAAACCGGTCACCTGGGCTGCGACGGCGGCTTAGGGGCAGAAGCGGCGGTCCAGGGCCGCCTGGCGCAGCAGCCTGTCCCAGCCGCGGTCCCTGCAGTCCCTCCCTGGCGGCTGCGCAGCCGTCCCACGACAGGGGCCATAAACTCTCCAGAGCGGAAAGCCGCACCCTGGTGGCCCGGCCCCGCGCCCAGACCTGGCGGCCGCTGGCACCTGACCCGCTGCATGGGTCTCCAGGGAGCTCGCTGCCCACCCGGCGCTGCAGGCTCGGCTCCCTCGTACACTCTCTGGTAGGTGCTAGGGACGACCCTATGGGCCAGCTTGCCATGCCCAGTCCCCAGGCCGCACCCACCCTGGCTCCCTGGGCTAGGGGACTGGCTCCTCCTGTGAGTCGTGGGTCTGGGAGGCAGGGGCGTTAGGGGAGAGTGAGGGACCGAGGGCAGCCCCTGCTGTGTGCACAGCGAGGTCGTGCACAGGCGTCTGTTGCAGAGCGTGCAGCTTCAGATGAGACTGGATTGCAGGTGGAGATGACTGTGGGTGCGCACACCTGGAGGTGAAGGGGAGGCAGCCTGTCTACCTGACCCATGAAATACAGGAGACTGTACCCCAGAAGCAGCGGGTTCACTGCTCCATTGATTAAGCAAGTCTGGGACACACATGTAGCTAAGCTGTGAGTTCTGTACCAGCGATCCCAACACCCACGCCCTCAGAAAGACACTGGTGTGGGGCCTGGGTGCTTGTCAGGCCTGAAAGTGGAGAGCACGGGCCAGAGACACTGAGTAGGGGGAACCCACCCTAGGGCTCTGAGGGACGACGATGTGGGGAGCTGGTGACAGAGCCTGAGCTGGCCCAATGTTGCACGGTGGGGACAGATTCGAGGTACAGTGGGGACTGGTGACCTCAGTTCCCAGTGTCCCAGCCTGGCCTCCCAGTCCACCCAGCAATTAGTGGGTGCTGCCCTGCAAAGACTCTGGGGGTGCCTCAGCCCTCCTCATCACACGTGACTGGTGACTTCTGTGTCCACCCGCACAATAAGAGGGATCTTCTCTCACTTTCAGGCAAGCCCAAGAAAGTCAGGGGCCTATGTGAGCCAAAGAGGAGAGAAGGTGATGCCTCAGCCCAGTGTTTCTGCCCCACCTCGCTTGTGGCCTTCGGAACTTGATTTGCACCGCAGGAAAATGGGCAATGAAAACCCCTCCCTAACTGGCTTCTCAGTCCACTCTGACCAGCCCACTGCACAGCGCCCACCCTGCAGCTCCAGGTACAGAGGCTGGGATGGCTCTGGGCTGACCTAAGGGCCTTCTGATGGCTCCAACCCTCGGGATGCCTCATGCTCACCCTTTGGCACCCACCTGACAGCTCAGCATCTCTGCTCTCTGCCATCCTCAATGCCTGCTCTAGACAAGCCCAAGTCCCCCAGGAGTGGCAGAGGGAACTGAGCCGAAAACTAAGTCTCGGCTCACTGAACCCCAAGTGGGCTGTCCAGCCTCGCCCTTCAGTTCACAACCCCAGGCAGGTTCCCTCCAGGGATGTGATCCCAGGGGCCACAGCAGCACATTCTGGCCTAACCTATCCACTATTTAAACAGTTACTGAAAAGGCCAGGATGGCCGTGGGCCCTGACATTAATCCCCTTTCTCTGTGAGGGGGCTGGGTTGGGTTTGCCATCCTGATGTCTTTGTGGAAAGAGCTGGCAGGTGAAGCAAGTCTCAGGGGCCAGCCATGGGACAAGGAACCTAGGACTGGCCTCTGCTGGAACCCTCTGAGGCCCCTGCGGACAGGAGGATCCAATGGAGGTCTAGCCACCCCTCCCAGGTTGGTGCTCACAGCCCCTCCCTGGCCCACTCCCTGCACACCTGCACCTGCTGGTCTCTGGGAGAGGAGCATCCATCCATCTTGTGCGCATAGCTTTCGGCTCCATTTTCATGAGGATGGTCTCCTTGGCAGAAATGCCCATTAGGGGATCCTGAGCCTGTGCTAGCTCTTCTCTAAGTGCCAAAGCCAGTGAGAGGGACTTGAAAACTCAAGACTTATTAACAGTATTTTCTGCATTTTGTGCTTTCAGGGTTGTTTTTTCCTTAAAATGTGTAAAAACAAACATTGAGATTTCTATCTTTTATATAATTTGGATTCTGTTATCACACGGACTTTTCCTGAAATTTATTTTTATGTATGTATATCAAACATTGAATTTCTGTTTTCTTCTTTACTGGAATTGTTAACTGTTTTATAGGCCAAATCTTTTAAAAAAAACACATCTCTCTAATTTCTCTAAACATTTCTAATTACATATATATTTACTATACCTAATACACTACTTTGGAATTCCTTGAGGCCTAAATGCATCGGGGTGCTCTGGTTTTGTTGTTGTTATTTCTGAATGACATTTACTTTGGTGCTCTTTATTTTGCGTATTTAAAACTATTAGATCGTGTGATTATATTTGACAGGTCTTAATTGACGCGCTGTTCAGCCCTTTGAGTTCGGTTGAGTTTTGGGTTGGAGAATTTTCTTCCACAAGGGATTGTCTTGGATTTTTCTGTTTCTCCCTCAATATCCACCTGGAAAACATTTCAATTAATTTATATTTACTTAAATATTTCTGTGCAAAAACTGTGTACAAAAGCCCCAAAGCATAATTTGTGCAGTTGAGCGCATGTTCTGTTGTTCAGCATTTATGGTGGTTGGTAGTGGAAAAGATTTTTAGAATATGTGGATTTTCGGGATATTCCCAGAAGCCCAGATAGCGACACTTTACCTTTGGAGGAATTACTTCTCAGAATATTGCACACAATCAATCGCCTTTGGAAGGAGCATATATCCCCAGCAAAAGCTCTGGTTTTTTGAAGTCTGTATTGTGTGTTACTTCCAGGAGAATATGCAATGATGACAATGTTATTAGATGATTCAAATATGAAGTGCTGTTATGCCAAACAATGAATCTTTGTGTTATACATTATGCCTAACTATAAATCTTTGTGTTATACATTTTAATGTCATTGGAGAGTACTCCTGTCTTCTTGGCATTATTGATAATTAGATTCTAATTGCTAATAAGTCAGAAAAATTAGGAACACCAAATTTCAGTTGTCTCAAAAGCACTCCTCTTATTAAATTTGGATGTTTACCTTTATCACATCAAAAGAAATATTGTTAGAAAGGTGTTTAATGTTTTGCAGATGGATAGATTACTGTTATTAGTTCTCATTTCATTGTTAATTTTTAAAACCATAAGGTTGGAAGTATCAATATGCCTTTCAATATACCTTAGTGGAATTTATTAAATTTTCATGGATGTCCTTTAGGGGGTTCAGGAAGTTATTTCTATTGCTAGATTTCTGGAAGATTTATCAGGAATGAGTGTCAGACATTGTCAGACGTCCATTGAAATCATCATGGTCTTTTCCTTTATTCTATTAATATGATGTATTACACTGATTGATTTTTAAATTTGTATTGGTAGGATAATTCCACTTGGTTATATTGTCTAACTTTTTTCTAATTTTCTTTCATTTTTATTACAGATGAGGCCTCACTCTGTCACCCAGGTTGGGGTGGAGTGGCACAGTCACAGCTCACTATAACCTCAAGCTCCTGGGCTCAAGTGATCCTGCCACCTCAGCCTCCTAAGTAGCTGGAACTACAGATGTGCACTGCCATGCCAGGCTTGTCTAACATTTTTATGTGTTGCTTCATCCAGTTTGCTAGAGTTTTTGGAGATTTCTGTCTTCATTCATGAGGGATAATAGTCTGCACTTTTATTTTCTTGTGATACTTTTGTCTGATTTGTTATCTGGGTAATACTGGCCTTGAAAATGAATTGATGTTTTCCTGCTTCTCTGCTTTGCAAGTGTTTGTGAAGGATTGGTTATTCATTAAGTGTTTAATAGAATTCACTAGTGAAGCTATGTGAGCCAGGGCTAGACTGATGAAGAGTTTTCATTAGTCTAATCTGTTTACTTGCTGTATAAGTACGCATATATTCTCTTTCTTCTTGATTTAATTTTACACTTTGTGTATAGCAGGGAATCTGTGTCTAATTTGTAGTATTTCATGCTTCTAGGTTTTCATGGCAGTTGAGATGTAAGAATAACAATAATGTTGGGAGAAGGAAGTTGTGGACAATCCATGAATATCCCAACATCTGTTGTAGGAAGGTTAAGATTACTTTTTTTTTTTTTGCTGTACTGAACTGAATACTCTTATTTATAATGTCAGACAAATGTAATGTTGTATATAAATAGAACTAGGAAAATGTGCCATTTGTCTTAGTATTTAATCAAGATGGAAGTCTGGGCCTACCTCCTCTCTTTTATTAATATGTAGACAGGACACCAACACAAATTAGAATGAAGACAAACAAAATGTTAGCAAATGAAGAATGGTATCAATTGGTTAAAATGTGATGAAATAGAGTGGTGAATATTTACATAGAATCCATGATGTGTTAGGTGCTATTTCAAGCTATTTGCACATATAGTTTTAATACCAATGACGTTAAAATGTATAACACAAAGATTCATATAAATAAAAATTACAACATTGTAAATAATATTAGGTGACACTAAAACTGTCATAGAAATACACATTTATATAAAACATAAAGTAACATGAAGTATTAAATTTTAGAAACTTTGATTACTAATCAGATGAACAACTGATTAGCCTTTTTATCCAGTAAAAAAGGCATACATATTATTTTCAAATTCCAGAGACAAATATTTTAAATATTGAAGTTGAAGACCTAAAAATGTGTCACTGACCTCATGGAAGTAGATATTCACTAGGTGATATTTTCTAGGCTCTCTGAAATTATATCAGAAAAATGTGAATTAGAATATAACCCATAAATAATATCTGGCCACATACAAAGTAATTGAAGATCAATTTAAATGGCTATTGGATTAAGAAATAGGGACTGAGGTAAATTTGCAGTGTCAGGGAGGATCTAAGGAGGAAGCATTGACACTGGAGCCCAAGGACCTGGGATCACAGAACAGATTCTACCAGTGCTAACTTACTGCTCCACAGAAAACATCAATTCTGCTCATGCGCAGGTACAATTCATCAAGAAAGGAATTACAACTTCAGAAATGTGTTCAAAATATATCCATACTTTGACATATTAATGAAGTAATCACATTCTACACATAACTACTCCATATGGAATACTGGGGAGGAGGTGTTCCAAATAAAGAGACTGAGGATTTCTCATGAGAACTCAGTGTCTGCTAGAAAATATCTAAGTAAAATATTTTACTTATGTGGAAAGTGTGGATGTTTGTGCATCAAAAGTTTCAAGAATCCCTAAAATTTACAATGGAGATGAGGAGAAAATATCAGAATTTCCCAGCACCAGAAATAAGGCAAGAAAAAATTCAGAGGGGTTGTAAATGTGAAAAGCCAATGGCTGGTCACACAGCAACATTGATAACCTTGTGCCTGGACAACTAGAATAAATACATAAACATACACATTGAAAATATTTCCAATATTAGATCTCCCTCATGTGAGAACTAAATTATAAAGATTGAAGCATAGAAGAAAATAAGCTACCAGAATAAATTTGATTACACATAAATTTCTGATATTGAAACTGTCACAAATGTTTAAGTTGGTAGTGGAAGACAAAGGACATATAATCTTGGGAGTCCTAAGGCCCTGCCCACTGCCAGTCCCTCCACACTACTACAGCTGATGCTTTCTGGAAATCACCACCTCCTGGCAGGAGCCCAACCAGCACAAATATAGAGCATTAAACCACCAAAGCTAAGGAGGCTCACAGAGTCTATTGCACCCTTCACCACCTCCACTGGAACAGGCGCTGGTATCCATGGCTCAGAGACCCAAAGATGGTTCACATCACAGGGCTCTATGCAGACAACCCCCAGTACCAGCCCAAAGCCACGTAGACCTGCTGGGTGGCTAGACCCAGAAGAGAGACAACAATCAATGCACTTTGGCTTACAGGAAGCCATGCCCATAGGAAAAAGGGGAGAGTACTACGTCAAGGGAACACCCCGTGGGATGAAAGAGTCTGAACAACAGTCTTCAGCCCTAGACCTTTCCTCTGACAGAGTCTACCAAAATGAGAAGGAACCAGAAAACCAACCCTGGTAATCTGACAAAACAAGAATCTTCAACACCCCCCAAAAAATCACACCAGTTCATCACCAATGGATCCAAACAAAGAAGAAATCACTGATTCATCTAAAAAAAAATTCAGGTTAGTTATTAAGCTAATCAGGGAGGGGCCAGAGAAAGATGAAGCCCAATGCAAGAAAATCCAAAAAATGATACAATACGTGAAGGGAGAATTATTCAAGGAAATAGATAGCTTAAATAAAAAAATAAAAAATCAGGAAACTTTGGACGTACTTTTAGAAATGTGAAATGCTCTGGAAAGTCTCAGCAATAGAATTGAACAAGTAGAAGAAAGAAATTCAGAATTCGAAGACAAGGTCTTTGATTTAACCCAATCCAATAAAGACAAAGAAAAAAGAATAAGAAAATATGAGCAAAGTCTCCAAGGAGTCTGGCATTCTGTTAAATGATGAAACCTAACACTAATTGGTGTACCTGAGGAAGAAGTGAATTCTAAAAGCCAGGAAAACATATTTGGGAGAATAATCTAGGAAAACTTCCATGGCCTTGTGAGAGACCTAGACATCCAAATACAAGAACCACAAATAACACCTGGGAAATTCATCACAAAAAGATCTTAGCCTAGGCACATTGTCATTAGGTTATCCAAAGTTAAGACAAAGGAAAGAATCTTAAGAGCTGTGAGACAGAAGCACTAGGTAACCTATAAAGGAAAACCTGTCAAATTAACAGCAGATTTCACAGCAGGAACCTTACAAGCTAGATGGGATTGGGGCCCTTTCTTCAGCCTCCTCAAACAAAACAATTATCAGCCAAGAATTTTGTATCCAGCAAAACTAAACATCATATATGAAGGAAAGATACAGTCATTTTCAGACAAACAAATGCTGACAGAATTTGCCATTACCAAGCCAGGACTCTAAGAACTGCTAAAAGGAGCTCTAAATCATGAAACAAATCCTGGAAACACATCAAAACAGAACTTCATTAACGCATAAATCACACAGGACCTATAAAACAAAAATACAAGTTAAAAAACAAAAACAAAGTACAGAGGCAACAAAGAGCATGATGAAAGCAATGGTACCTCACTTTTTAATACTAATGTTGGTTGTAAATGGCTTAAATGCTCCACTTACAAGATACAGAACCACAGAATGGATAACAACTCACCAACTAACTATCTGCTGCCTTCAGGAGACTCACCTAACACATAACGACTTACATAAACTTAAGGAAAGTGGTAGAAAAAGGCATTTCATGCAAATGGACACCAAAAGCAAGCAGCAGTAACTATTCTCATATGAGACAAAACAAACTTTAAAGCAACAGTAGCTAAAAGAGACAAAGAGAGACAGTATATCATCTGTCACCTGACAGTCTCATCCAACAGAAAAATATGACAATCCTAAACATATGTGAACCTAACACTGGAGCTCCCAAATTTATAAAACAATTACTAGTAGACATAAGAAATAAGATAGACAGCAACACAATAATAGTGGGGGACTTCAATACTCCACTGACAGCACTAGACAGGTCATCAAGACAGAAAGTCAACAAAGAAACAATGGATTTAAACTATACTTTGGAACAAATGGACTTAACAGATATATATAGAACATTTCATCCAACAACCACAGAATACACATTCTATTCAACAGCACATGGAATTTTCTCCAAGATAGACCATATGATAGGCCATAAAATGAGTCTCAATAAATTTAAGAAAATTGAAATTGTATCACGCACTCTCTCACATCACAATGGAATAAAACTGAAAATCAACTCCAAAAGGAATCTTCGAAACCATGCAAATACATGGAAATTAAATAACCTGCTCCTGAATGAGCATTGGGTGAAAAACGAAATCAAGATGGAAATGTAAAAAATTTCTTCGAACTGGATGACACAACCTATCAAGACCTCTGGGATACAGCAAAGGCAGTGCTAAGAGGAAAGTTTATAGCACTAAACACCTACGTCGAAAAGTCTGAAAGAGCACAGACAATCTAAGTTCACATCTCAGGGAACTAGAGAAGGAGGAACAAGCCAAACCCAATCCCAGCAAACAAAGGAAATAACCAAGATCAGAGCAGAACTAAATGAAATTGACACAACAACAACAACAACAAAAATACAAAACATAAATAAAACAAAAATTTGGTTATTTGAAAAGATA'

def findStopCodon(dnaStr, startIndex, stopCodon):
    currIndex = dnaStr.index(stopCodon, startIndex+3)
    while (currIndex != -1):
        diff = currIndex - startIndex
        if (diff % 3 == 0):
            return currIndex
        else:
            currIndex = dnaStr.index(stopCodon, currIndex+1)
   return -1

def findGene(dna, where):
    startIndex = dna.index('ATG', where)
    if startIndex == -1:
        return ''
    taa_index = findStopCodon(dna, startIndex, 'TAA')
    tag_index = findStopCodon(dna, startIndex, 'TAG')
    tga_index = findStopCodon(dna, startIndex, 'TGA')
    minIndex = 0
    if (taa_index == -1 | (tga_index != -1 & tga_index < taa_index)):
        minIndex = tga_index
    else:
        minIndex = taa_index
    if (minIndex == -1 | (tag_index != -1 & tag_index < minIndex)):
        minIndex = tag_index
    if minIndex == -1:
        return ""
    return dna[startIndex:minIndex + 3]

def printAllGenes(dna):
    startIndex = 0

    while True:
        currentGene = findGene(dna, startIndex)
        if len(currentGene) == 0:
            break

        print(currentGene)
        startIndex = dna.index(currentGene, startIndex) + len(currentGene)

printAllGenes(gene_sequence)

它输出了29个基因，我不确定能找到多少基因。下面一行中的错误导致它在通过其余部分之前结束。

 currIndex = dnaStr.index(stopCodon, currIndex+1)

Answer 1

您似乎错误地认为.index()在找不到子字符串时返回-1：

currIndex = dnaStr.index(stopCodon, startIndex+3)
while (currIndex != -1):

情况并非如此，它会引发错误：

>>> help(str.index)
Help on method_descriptor:

index(...)
    S.index(sub[, start[, end]]) -> int

    Like S.find() but raise ValueError when the substring is not found.

>>>

如帮助说明所述，您确实需要.find()方法。

让我们尝试简单地编写代码，而不是仅修补它：

gene_sequence = 'AAC...ATA'  # supply your original sequence here

STOP_CODONS = {'TAA', 'TAG', 'TGA'}

def findStopCodon(dnaStr, startIndex, stopCodons):

    for currIndex in range(startIndex + 3, len(dnaStr), 3):
        if dnaStr[currIndex:currIndex + 3] in stopCodons:
            return currIndex

    return -1

def findGene(dna, where):
    startIndex = dna.find('ATG', where)

    if startIndex == -1:
        return '', startIndex

    stopIndex = findStopCodon(dna, startIndex, STOP_CODONS)

    if stopIndex == -1:
        return '', stopIndex

    return dna[startIndex:stopIndex + 3], stopIndex + 3

def printAllGenes(dna):
    startIndex = 0

    while True:
        currentGene, startIndex = findGene(dna, startIndex)

        if not currentGene:  # empty strings are False
            break

        print(currentGene)

printAllGenes(gene_sequence)

这输出69个基因并且不会破坏。测试它以确保它真正做到你想要的。

Python字符串索引/打印错误

1 个答案: