Changing output format for hamming distance of FASTA sequences (using Biopython)

Question

[nameuser]

Hi there, I currently have the code stated below. The output I currently have it set to write out is not what I'm looking for. However, this has been the only way I have successfully run the script. I would like to remove the sequences from a fasta file that have a hamming distance of 50 or more. I tried to use an additional for loop and write the output file with SeqIO but the way 'seqs' is currently written, it was not defined. I created an empty list and tried to append the results.

from Bio import SeqIO
REFERENCE_SEQ = 'ATGC.....'

def hamming_distance(seq):
    result = sum(b1 != b2 for b1, b2 in zip(REFERENCE_SEQ, seq))
    return result


 if __name__ == '__main__':
     filename = open('test.fasta', 'r')
    seqs = [record for record in SeqIO.parse(filename, 'fasta')]

     counted = list(map(lambda x: (x, hamming_distance(x)), seqs))
     results = list(filter(lambda x: x[1] < 50, counted))
     print(*results, sep='\n', file=open("output.fasta", "a"))

The current output is as follows:

(SeqRecord(seq=Seq('TCGCCCTTGCTCACCATGCTAGGTTCTCCTTCTTAATCTAGAATGCAATATACT...CGG',SingleLetterAlphabet()), id='rev_comp_consensus', name='rev_comp_consensus', description='rev_comp_consensus', dbxrefs=[]), 7)
(SeqRecord(seq=Seq('TCGCCCTTGCTCACCATGCTAGGTTCTCCTTCTTAATCTAGAATGTAATATACT...CCG',   SingleLetterAlphabet()), id='1', name='1', description='1', dbxrefs=[]), 7)
(SeqRecord(seq=Seq('TCGCCCTTGCTCACCATGCTAGGTTCTCCTTCTTAATCTAGAATGCAATATACT...GGT',   SingleLetterAlphabet()), id='2_also7', name='2_also7', description='2_also7', dbxrefs=[]), 7)

Etc.

Please let me know if you have any ideas to

1. remove the sequences with a specified hamming distance

2. write the remaining sequences to a fasta file

Thank you so much.

[cschu181]

Are the three final lines of code indented properly?

[nameuser]

oops, must've missed that when I wrote the question. I just fixed their indentation! Thanks.

[cschu181]

Does this work?

with open("out.fasta", "w") as f:
    for record in SeqIO.parse(open("test.fasta"):
        dh = hamming(str(record.seq))
        if dh < 50:
            print(">{id}\n{seq}".format(id=record.id, seq=record.seq), file=f)

[nameuser]

The logic definitely makes sense to me, I adjusted it a little for errors but the print line was extremely helpful! I'm getting a blank output right now though, when I did a matrix for the sequences, there were plenty (500,000 sequences per file) with less than 50. Additionally, dh is being defined.

Thanks again!

[cschu181]

Could you post the corrections you've made, please?

[nameuser]

 if __name__ == '__main__':
    with open(filename + "out.fasta", "w") as f:
        for record in (SeqIO.parse(filename, 'fasta')):
          if hamming_distance(str(record.seq)) < 50 :
                print(">{id}\n{seq}".format(id=record.id, seq=record.seq), file=f)

Answer 1

[Joe]

I assume this is a follow-on from this thread? C: Counting mismatched characters from sequences from a fasta file in comparison to

If so, I gave you workable code, you just need to modify the output format and/or use SeqIO.write() as I suggested at the time.

from Bio import SeqIO
import sys

def hamming_distance(s1, s2):
    """Return the Hamming distance between equal-length sequences"""
    if len(s1) != len(s2):
        raise ValueError("Undefined for sequences of unequal length")
    return sum(ch1 != ch2 for ch1, ch2 in zip(s1, s2))

similar_seqs = []
for i, record in enumerate(SeqIO.parse(sys.argv[1], 'fasta')):
    if i == 0:
        reference = record
    if hamming_distance(reference.seq, record.seq) < 50:
        similar_seqs.append(record)

with open("similar_seqs.fasta", "w") as output_handle:
    SeqIO.write(similar_seqs, output_handle, "fasta")

Input:

Note, I've added a modified entry at the end with 3 residues altered

>Zebrafish
ESLLRFGLRSDLDFRLSLNGKEDLLDTGQSLSSCGVVSGDLISVILPASSQTSSAAHQTH
TDQQSSQECVDLQQDCMDQQQQQEQECVCAAAPPLLCCEAEDGLLPLALERLLDSSTCRS
PSDCLMLALHLLLLETGFIPQGGAVSSGEMPIGWQAAGVFRLQYVHPLLENSLVSVVAVP
MGQTLVINAVLKMETSLENSRKLLLKPDEYVTAWTGGSSGVVYRDLRRLSRLVRDQLVYP
LMATARQALGLPLLFGLPVLPPELLLRLLRLLDVRSLVSLSAVCRHLNTATHDASLWRHL
LHRDFRVSFPAHRDTDWRELYKQKYRQRAARRGRHWFYPPPISPLIPFPSSPALYPPGII
GDYDQMPILPRPRFHPIGPLPGMSAPV
..... Tuncated for character count....
>Anole
QALLSWGYSSETKFEITLNNKDSLVGDQDTLASFGIVSGDLICLILEDDASSPSSSLPSS
QSNHHSGPSQEFTSEGGPDDLDLQEATGSFPSEPMLCCEATDGQVPHSLQTLYHSAECTN
ANDALIVSIHLIMMETGYVPQGTEAKASSMPENWRNKGVYKLLYTHPLCENGFAVLTCVP
LGNLIVVNAMLKITSDIKSVKRLQLLPTSFICFQDSANVVGVYKDLQKLSRLFKDRLVYP
LLAAARQALNLPDVFGLVVLPLELKLRIFRLLDFRSLLSLSAVCHDLYAASNDQLLWRFI
YLRDFRDPVARSRDTDWKELYKKKMKQKDALRWRHMMFLPPLHPNPLYPNPFPLYPPMII
GEMDERPSLFPSHLDPFGSFQNPNPTL
>Human
QSLLTWGYSSNTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIIPSSTSEHSS
LQNNSNGPSQNFEAESIQDNAHMAEGTGFYPSEPMLCSESVEGQVPHSLETLYQSADCSD
ANDALIVLIHLLMLESGYIPQGTEAKALSMPEKWKLSGVYKLQYMHPLCEGSSATLTCVP
LGNLIVVNATLKINNEIRSVKRLQLLPESFICKKLGENVANIYKDLQKLSRLFKDQLVYP
LLAFTRQALNLPDVFGLVVLPLELKLRIFRLLDVRSVLSLSAVCRDLFTASNDPLLWRFL
YLRDFRDNTVRVQDTDWKELYRKRHIQRESPKGRFVMLLPPFYPNPLHPRPFPRLPPGII
GEYDQRPSLIPPRFDPVGPLPGPNPIL
>Zebrafish_modified
ESLLRFGLRSDLDFRLSLSGKEDLLDTGQSLSSCGVVSGDLISVILPASSQTSSAAHQTH
TDQQSSQECVDLQQDCMDQQQQQEQECVCAAAPPLLCCEAEDGLLPLALERLLDSSTCRS
PSDCLMLALHLLLLETGFIPQGGAVSSGEMPIGWQAAGVFRLQYVHPLLENSLVSVVAVP
MGQTLVINAVLKMETSLANSRKLLLKPDEYVTAWTGGSSGVVYRDLRRLSRLVRDQLVYP
LMATARQALGLPLLFGLPVLPPELLLRLLRLLDVRSLVSLSAVCRHLNTATHDASLWRHL
LHRDFRVSFPAHRDTDWRELYKQKYRQRAARRGRHWFYPPPISPLIPFPSSPALYPPGII
GDYDQMPILPRPRFHPIGPLPGMSAPL

Output:

$ cat similar_seqs.fa

>Zebrafish
ESLLRFGLRSDLDFRLSLNGKEDLLDTGQSLSSCGVVSGDLISVILPASSQTSSAAHQTH
TDQQSSQECVDLQQDCMDQQQQQEQECVCAAAPPLLCCEAEDGLLPLALERLLDSSTCRS
PSDCLMLALHLLLLETGFIPQGGAVSSGEMPIGWQAAGVFRLQYVHPLLENSLVSVVAVP
MGQTLVINAVLKMETSLENSRKLLLKPDEYVTAWTGGSSGVVYRDLRRLSRLVRDQLVYP
LMATARQALGLPLLFGLPVLPPELLLRLLRLLDVRSLVSLSAVCRHLNTATHDASLWRHL
LHRDFRVSFPAHRDTDWRELYKQKYRQRAARRGRHWFYPPPISPLIPFPSSPALYPPGII
GDYDQMPILPRPRFHPIGPLPGMSAPV
>Zebrafish_modified
ESLLRFGLRSDLDFRLSLSGKEDLLDTGQSLSSCGVVSGDLISVILPASSQTSSAAHQTH
TDQQSSQECVDLQQDCMDQQQQQEQECVCAAAPPLLCCEAEDGLLPLALERLLDSSTCRS
PSDCLMLALHLLLLETGFIPQGGAVSSGEMPIGWQAAGVFRLQYVHPLLENSLVSVVAVP
MGQTLVINAVLKMETSLANSRKLLLKPDEYVTAWTGGSSGVVYRDLRRLSRLVRDQLVYP
LMATARQALGLPLLFGLPVLPPELLLRLLRLLDVRSLVSLSAVCRHLNTATHDASLWRHL
LHRDFRVSFPAHRDTDWRELYKQKYRQRAARRGRHWFYPPPISPLIPFPSSPALYPPGII
GDYDQMPILPRPRFHPIGPLPGMSAPL

The reference sequence will always be included at present, but its easy to modify this to remove this if necessary.