Got 'TypeError:字符串索引必须是整数‘比较蛋白质序列

Question

如何按字母顺序返回列表？

我有序列翻译器，和一个可以读取dna和蛋白质序列的python代码。代码读取dna序列并将其翻译为蛋白质序列，读取蛋白质序列，将其与翻译的蛋白质序列进行比较，并打印出存在于读取的蛋白质序列中的蛋白质序列的列表。我如何打印它们中都存在的蛋白质的列表？

def translate_codon(cod):
    """Translates a codon into an aminoacid using an internal dictionary with the standard genetic code."""
    tc = {"GCT":"A", "GCC":"A", "GCA":"A", "GCG":"A",
          "TGT":"C", "TGC":"C",
          "GAT":"D", "GAC":"D",
          "GAA":"E", "GAG":"E",
          "TTT":"F", "TTC":"F",
          "GGT":"G", "GGC":"G", "GGA":"G", "GGG":"G",
          "CAT":"H", "CAC":"H",
          "ATA":"I", "ATT":"I", "ATC":"I",
          "AAA":"K", "AAG":"K",
          "TTA":"L", "TTG":"L", "CTT":"L", "CTC":"L", "CTA":"L", "CTG":"L",
          "ATG":"M", "AAT":"N", "AAC":"N",
          "CCT":"P", "CCC":"P", "CCA":"P", "CCG":"P",
          "CAA":"Q", "CAG":"Q",
          "CGT":"R", "CGC":"R", "CGA":"R", "CGG":"R", "AGA":"R", "AGG":"R",
          "TCT":"S", "TCC":"S", "TCA":"S", "TCG":"S", "AGT":"S", "AGC":"S",
          "ACT":"T", "ACC":"T", "ACA":"T", "ACG":"T",
          "GTT":"V", "GTC":"V", "GTA":"V", "GTG":"V",
          "TGG":"W",
          "TAT":"Y", "TAC":"Y",
          "TAA":"_", "TAG":"_", "TGA":"_"}
    if cod in tc:
        return tc[cod]
    else:
        return '-1'


def seq_prot(dna_seq, ab):
    seqm = dna_seq.upper()
    prot = ab.upper()
    seq_aa = ''
    for pos in range(0, len(seqm)-2,3):
        cod = seqm[pos:pos+3]
        seq_aa += translate_codon(cod)
    for p in seq_aa:
        if p in prot:
            seq_aa[p] += 1
        else:
            seq_aa = p

    return seq_aa

dna_seq = "ACCCCTGTGACATACCTTTATGTTGCCTCGGCGGATCAGCCCGCGCCCC"
ab = 'TLYPAP'

print("The protein sequence are :",seq_prot(dna_seq, ab))

蛋白质序列为: TYPP

Answer 1

您的代码被破坏了，因为它将seq_aa视为str和dict。

def seq_prot(dna_seq, ab):
    sequence = dna_seq.upper()
    protein = ab.upper()
    matches = {}

    for position in range(0, len(sequence), 3):
        codon = sequence[position: position + 3]
        aa = translate_codon(codon)

        if aa in protein:
            if aa in matches:
                matches[aa] += 1
            else:
                matches[aa] = 1

    return matches

dna_seq = "ACCCCTGTGACATACCTTTATGTTGCCTCGGCGGATCAGCCCGCGCCCC"
ab = 'TLYPAP'

print("The protein sequence matches are :", seq_prot(dna_seq, ab))

输出

The protein sequence matches are : {'T': 2, 'P': 3, 'Y': 2, 'L': 1, 'A': 3}

您可以通过在返回的dict上使用.keys()来从中提取蛋白质。如果要将字母与值相乘，可以使用乘法(*)作为重复运算符。然而，任何有条理的感觉都已经丢失了--我们只是在处理存在。如果你想维持秩序，我们必须采取不同的方式。