Biopython: Extract CDS from modified GenBank records?

Question

I have some basic familiarity with python and have been extracting coding sequences from genbank records. However, I'm unsure how to handle records where the coding sequence has been modified (e.g. owing to correcting internal stop codons). An example of such a sequence is this genbank record (or accession: XM_021385495.1 if the link does not work).

In this example, I can translate the two coding sequences that I can access, but both have internal stop codons - and according to the notes also indels! This is the way I have accessed the CDS: 1 - gb_record.seq 2 - cds.location.extract(gb_record) for where feature == "CDS"

However, I need the sequence that has been corrected. As far as I can tell, I think I need to use the "transl_except" tags in the CDS feature but I am at a loss how to do this.

I wonder if anybody might be able to provide an example or some insight of how to do this?

Thanks

Jo

Answer 1

I've got some demo code written in python3 that should help explain this GenBank record.

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:]

Code output:

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

From the note section of the CDS, we have: inserted 5 bases in 4 codons; deleted 2 bases in 2 codons; substituted 11 bases at 11 genomic stop codons".

How does this relate to our output? The reading frame never changes, suggesting that the 2 deleted bases are absent from the given nucleotide sequence. Five unknown nucleotides (N) exist in 4 codons (unknown amino acid, X). The authors of the sequence have accounted for indels. Eleven premature stop codons are present, which are simply translated as unknown amino acids. The "transl_except" tags match the locations of the premature stop codons. The nucleotides at these sites have not been altered. The authors provide XP_021241170 as a possible corrected translation product, but it's still very bad.