biopython - Biopython：从修改后的 GenBank 记录中提取 CDS？

我有一些用 python3 编写的演示代码，应该有助于解释这个 GenBank 记录。

import re

aa_convert_codon_di =  {
    'A':['[GRSK][CYSM].'],
    'B':['[ARWM][ARWM][CTYWKSM]', '[GRSK][ARWM][TCYWKSM]'],
    'C':['[TYWK][GRSK][TCYWKSM]'],
    'D':['[GRSK][ARWM][TCYWKSM]'],
    'E':['[GRSK][ARWM][AGRSKWM]'],
    'F':['[TYWK][TYWK][CTYWKSM]'],
    'G':['[GRSK][GRSK].'],
    'H':['[CYSM][ARWM][TCYWKSM]'],
    'I':['[ARWM][TYWK][^G]'],
    'J':['[ARWM][TYWK][^G]', '[CYSM][TYWK].', '[TYWK][TYWK][AGRSKWM]'],
    'K':['[ARWM][ARWM][AGRSKWM]'],
    'L':['[CYSM][TYWK].', '[TYWK][TYWK][AGRSKWM]'],
    'M':['[ARWM][TYWK][GRSK]'],
    'N':['[ARWM][ARWM][CTYWKSM]'],
    'O':['[TYWK][ARWM][GRSK]'],
    'P':['[CYSM][CYSM].'],
    'Q':['[CYSM][ARWM][AGRSKWM]'],
    'R':['[CYSM][GRSK].', '[ARWM][GRSK][GARSKWM]'],
    'S':['[TYWK][CYSM].', '[ARWM][GRSK][CTYWKSM]'],
    'T':['[ARWM][CYSM].'],
    'U':['[TYWK][GRSK][ARWM]'],
    'V':['[GRSK][TYWK].'],
    'W':['[TYWK][GRSK][GRSK]'],
    'X':['...'],
    'Y':['[TYWK][ARWM][CTYWKSM]'],
    'Z':['[CYSM][ARWM][AGRSKWM]','[GRSK][ARWM][AGRSKWM]'],
    '_':['[TYWK][ARWM][AGRSKWM]', '[TYWK][GRSK][ARWM]'],
    '*':['[TYWK][ARWM][AGRSKWM]', '[TYWK][GRSK][ARWM]'],
    'x':['[TYWK][ARWM][AGRSKWM]', '[TYWK][GRSK][ARWM]']}

dna_convert_aa_di = {
    'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
    'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
    'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
    'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
    'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',
    'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
    'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',
    'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
    'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',
    'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
    'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
    'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
    'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',
    'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
    'TAC':'Y', 'TAT':'Y', 'TAA':'*', 'TAG':'*',
    'TGC':'C', 'TGT':'C', 'TGA':'*', 'TGG':'W'}


dna_str = "ATGACCGAGGTGCAAGACCTTGCACTTGGATTTGTTGAACCTCATGAGGTTCCCCTGGGCCCCTGGACATCGCCTTTTTCCAGCGTTCCACCAGAGACTTCACCCAACTGCTGTGACTTTTCAAACATCATTGAGAGCGGCTTGATACAGTTAGGCCACTCTCGCAGCTGTGAAGTTGTGAAGGCAAACTCCAGCGACCCATTCCTTCTTCCTTCAGAAAAGCAACTCGAGGAGCAGCGGGAGGAAACCCAGCTCTATCCTGCAGCGAGCGGGGCTGCGCAAGAGGCAGGTGCTGCTCTCACGGCCCGAAGGCAGCTCCGAGCTGCCGGGTGCGGTCACGTCAGCGGCCGAGCTGCCCGGCGGGGTGTGCATAAGAGCGAGCTATATGTGCTGCGTGTCATCACGGAGCCTTTCAAGTCCCTCCCTCCTTCTCCACTGCTGGGGCTGCAGTGGGCACCGGGCAGGAGGAGCGGCCGCAGCCCCGCGGGGGTGGGACGAGTCTCTGGGGGCTGCGCCACTTGGAAGATTTGCATTGGGTACATTGATAGCATTGTGATTGATGGCCTATTTAATACCATAATGTGTTCTTTAGATTTCTTTTTGGAGAACTCAGAAGAAAATTTGAAGCCAGCTCCACTTTTTCCAGCACAAATGACCCTTACTGGCACAGAAATTCATTTTAAACTTTCTCTAGATAAAGAGGCTGATGATGGCTTTTATGACCTTATGGATGAACTACTGGGTGATATTTTCCGAATGTCTGCCCAAGTGAAGAGACTAGAAGCCCACCTGGAATCAGAACATTAGGAGGACTATATGAACAGTGTGTTTGATCTGTCTGAACTCAGGCAGGAGAGTATGGAGAGAGTAATAAACGTCACCAACAAGGCCTTGAAGTACAGAAGATCTCATGATAGCTATGCTTATCTCTGACTAGAGGATCAGCTTGAGTTTATGAGGCAATTTCTTCCTTGTGCTCGTGGTTTAATGTCCACACAGATATCTCTTACTGGCATCCCACTACTAAACTGTGTAAAAAGCAGGCAAGAAAGAAACTAGTTTAAATAACTTCCTATTTATGAAAATCTCTGTGTTCAGATGAGTAAGTTTGAAGACCCAAGAATTTTTGAAAGCTGGTTTAAGGTGATTATGAAGCCTTTCAAAATGACACTTCTAAACATTACTAAGAAGTGGAGCTGGATGTTTAAGTAGTACACTATAGAAATAATAAGATTGAGTCTGAATGACTTCAAAGACTTTATAAAAGTGACAGATGCTGGACTTCAAAGAGGGAGGCATTATTGTGCACTGGCAGAAATCACCGGTCACCTCTTGGCTGTGAAAGAGAGGCAGACAGCTGCTGGTGAATCCTTTGAACCTTTAAAAGAANTTGTTGCATTGTTGGAAAGCTACAGACAGAAGATGCCAGATCAAGTTTGCATCCAGTGTCAAATCAGTTGTATCCTGGGAGCCTTTAAGGGTTATGTACTTCTGGTTGGAGTAGGTGGTAGTGATAAATGAAGCTTGTCAAGGCTGGCAGCATGCATCTCTTCCCTGGAGGTCTTTTAAATCATATGGAAGAAAGACCATGAGAGCAAGAACCTGAAGGTAGATGTTGCCAGTTTGTGCATCAAGACTGGTGCCAAGAACATGCCCACAGTGTTTTTGCTGACAGATGCCCAGGTTCCAGATGAACGCTTTCTTGTGCTGATTAATGACTTGTTGGCATCAAGAGATCTTCCTGATCTGTTCAGTGGTGAAGATGAGGAGGGCAAAGTTGCAGGAGTCAGAAAAGAAGTCNNCCTGGGCTTGATGGACACCACAGAAAGCTGCTGGAGGTGGTTCTTTGGTAGAGCGCAGCAGCTGTTAAAAGTGTATGGTGAAGTAGAGTCGAAATGTTGTGCACTGGTCCAGGCAAATACAAAATTAGCAACAGCTAAAGAGAATCTAGAAACAATCTTGAAAAAGCTTATTTCTGAAAATGTGCATTGGAGCCAATCTGTTGAAAACCTCAAAGCATAAAAGAAAACTGTACTCAAGGATGTTACATCAGCAGCAGCGTTTGCATCTTTCTTTGGAGCCTTCACAAAACCATATAGTCAAGAACAGATGGAACATTTCTGGATTCTTTCTCTAAAGTCACAGGAGTGTCCTGTTCCTGTGATAGAGGGGCCAGACTCTGCCATCCTGATGAATGATGCTCCAAGAGCAGCACAGAGTAACAAGAGTCTGCTTGCTGATAGGGTGTCAGCAGAAAATGCCACTGCTCTGACACACTGTGAGCAGGGCCCTCTGATGATAGATCCCCAGAAACAGGGAATTGAATGGACACAGAATAAATACAGAACTGACTTTAAAGTCATGCATCTAGGAGAGAATGGTTATGTGTGTACTATTGATACAGCTTTGGCTTGTGGAGAGATTATACTAATTGAAAACATGGCTGAATCTATCGATCTCTTACTTGATCCCCTAACTGGAAGACATACAGGTAAAAGGGGAAGGAATACTTGCGCAATCAGAATTTCTTGAAGACAAAAAAAAAAAAAGTGTGAATTCTACAGGAATTTCCATCTCATCCTTCACACTAAGCTGGCTAACCCTCCCTGCAAGCCAGAGCTTNAGGCTCAGACCACTCTCATTATTTTCACAGATACCAGGGGCAGGCTGGAAGAACAGCTGTTGGCTGAGGTGGTGAGTGCTGAAAGGCCTGACTTGGAAAACCATACGTCAGCACTGGCGAAACAGAAGAGTGTCTCTGAAATCAAGCCCAAGCAGCTTGAGGACAACATGCTGCTCAGTCTGTCAGCTGCCCAGAGCACTTTTGTAGGTGACAGTGAACTTGAAGAGAAATTCAAGTCAACTGCAGGAGAAATGATTGTCCGCCCACATGTTCACAGCTTCTTATTTTGGCAAAAAGCTTCCACTGTAGACTCTGGAAGATTTCATATCTCTTTAGGACAAGGGCAGGAGATGGTTGTGGAGNGACAACTTGAGAAGGCTGCCAAGCCTGGCCACTGGCTTCTTCTCCAAAATATTAATGTGGTAGCCAAGTGGCTAGGAACCTTGGAAAAACTCCTCGAGCAATAGAGTGAAGAAAGTCACTGGTATTTCCGTGTCTTCACTAGTGCTGAACCAGCTCCAGCCCCAGAAGAGCACATCATTCTTCAAGGAGTACTTGAAAACTGAATTAAAATTACCAGACTATCAATAACACTGCCAGTTGTTAAGTGGATAAATGTATTCCTTTTTTTCCTTTGGCAGGATACCCTTGAACTGTGTGGCAAAGAACAGGAATTTAAGAGCATTCTTTTCTCCCTTCGTTATTTTCACACCCGTGTTGCCAGCAGACTCATTTGGCCTTCCAGGCTGCAATTAAGATACCCATACAATACTAGAGATCTCACTGTTTGCATCAGTGTGCCCTGCAACTATTTAGACACTTACACAGAGGTCAGACGCAGTGGTCAGAAAAACAAGTCTATAAAATCAGCTGATTCCAACCCTTAG"
aa_str = "MTEVQDLALGFVEPHEVPLGPWTSPFSSVPPETSPNCCDFSNIIESGLIQLGHSRSCEVVKANSSDPFLLPSEKQLEEQREETQLYPAASGAAQEAGAALTARRQLRAAGCGHVSGRAARRGVHKSELYVLRVITEPFKSLPPSPLLGLQWAPGRRSGRSPAGVGRVSGGCATWKICIGYIDSIVIDGLFNTIMCSLDFFLENSEENLKPAPLFPAQMTLTGTEIHFKLSLDKEADDGFYDLMDELLGDIFRMSAQVKRLEAHLESEHXEDYMNSVFDLSELRQESMERVINVTNKALKYRRSHDSYAYLXLEDQLEFMRQFLPCARGLMSTQISLTGIPLLNCVKSRQERNXFKXLPIYENLCVQMSKFEDPRIFESWFKVIMKPFKMTLLNITKKWSWMFKXYTIEIIRLSLNDFKDFIKVTDAGLQRGRHYCALAEITGHLLAVKERQTAAGESFEPLKEXVALLESYRQKMPDQVCIQCQISCILGAFKGYVLLVGVGGSDKXSLSRLAACISSLEVFXIIWKKDHESKNLKVDVASLCIKTGAKNMPTVFLLTDAQVPDERFLVLINDLLASRDLPDLFSGEDEEGKVAGVRKEVXLGLMDTTESCWRWFFGRAQQLLKVYGEVESKCCALVQANTKLATAKENLETILKKLISENVHWSQSVENLKAXKKTVLKDVTSAAAFASFFGAFTKPYSQEQMEHFWILSLKSQECPVPVIEGPDSAILMNDAPRAAQSNKSLLADRVSAENATALTHCEQGPLMIDPQKQGIEWTQNKYRTDFKVMHLGENGYVCTIDTALACGEIILIENMAESIDLLLDPLTGRHTGKRGRNTCAIRISXRQKKKKCEFYRNFHLILHTKLANPPCKPELXAQTTLIIFTDTRGRLEEQLLAEVVSAERPDLENHTSALAKQKSVSEIKPKQLEDNMLLSLSAAQSTFVGDSELEEKFKSTAGEMIVRPHVHSFLFWQKASTVDSGRFHISLGQGQEMVVEXQLEKAAKPGHWLLLQNINVVAKWLGTLEKLLEQXSEESHWYFRVFTSAEPAPAPEEHIILQGVLENXIKITRLSITLPVVKWINVFLFFLWQDTLELCGKEQEFKSILFSLRYFHTRVASRLIWPSRLQLRYPYNTRDLTVCISVPCNYLDTYTEVRRSGQKNKSIKSADSN"

mod_dna_str = ""
mod_aa_str = aa_str[:]
start = 0

for index in range(start, len(dna_str), 3):
    codon = dna_str[index:index+3]
    if len(mod_aa_str) == 0:
        break
    if codon in dna_convert_aa_di and dna_convert_aa_di[codon] == mod_aa_str[0]:
        mod_aa_str = mod_aa_str[1:]
    else:
        codon_match = "|".join(aa_convert_codon_di[mod_aa_str[0]])
        if len(re.findall(codon_match, codon)) > 0:
            print(index, codon_match, codon)
            mod_aa_str = mod_aa_str[1:]

代码输出：

804 ... TAG
930 ... TGA
1056 ... TAG
1065 ... TAA
1209 ... TAG
1389 ... NTT
1518 ... TGA
1566 ... TAA
1800 ... NNC
2019 ... TAA
2529 ... TGA
2622 ... NAG
2985 ... NGA
3087 ... TAG
3186 ... TGA

从 CDS 的注释部分，我们有：在 4 个密码子中插入 5 个碱基；删除了 2 个密码子中的 2 个碱基；在 11 个基因组终止密码子处取代了 11 个碱基”。

这与我们的输出有什么关系？阅读框永远不会改变，这表明给定的核苷酸序列中不存在 2 个缺失的碱基。5 个未知核苷酸 (N) 存在于 4 个密码子（未知氨基酸，X）中。该序列的作者已经考虑了插入缺失。存在 11 个过早终止密码子，它们被简单地翻译为未知氨基酸。“transl_except”标签匹配过早终止密码子的位置。这些位点的核苷酸没有改变。作者提供XP_021241170作为可能的更正翻译产品，但它仍然非常糟糕。

biopython - Biopython：从修改后的 GenBank 记录中提取 CDS？

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