Find sequence IDs of DNA subsequences in DNA-sequences from FASTA-file - biopython

Question

I want to make a function that reads a FASTA-file with DNA sequences(possibly ambiguous) and inputs a subsequence that returns all sequence IDs of the sequences that contain the given subsequence.
To make the script more efficient, I tried to use nt_search to make give all possibilities of the ambiguous sequence from the FASTA. This seemed more efficient than producing all unambiguous possibilities, especially for larger sequences an FASTA-files.
Right now, I'm struggling to see how I can check whether the subsequence is part of the output given bynt_search.
I want to see if eg 'CGC' (input subsequence) is part of the possibilities given by nt_search: ['TA[GATC][AT][GT]GCGGT'] and return all sequence IDs of sequences for which this is true.
What I have so far:
def bonus_subsequence(file, unambiguous_sequence):
seq_records = SeqIO.parse(file,'fasta', alphabet =ambiguous_dna)
resultListOfSeqIds = []
print(f'Unambiguous sequence {unambiguous_sequence} could be a subsequence of:')
for record in seq_records:
d = Seq.IUPAC.IUPACData.ambiguous_dna_values
couldBeSubSequence = False;
if unambiguous_sequence in nt_search(unambiguous_sequence,record):
couldBeSubSequence = True;
if couldBeSubSequence == True:
print(f'{record.id}')
resultListOfSeqIds.append({record.id})
In a second phase, I want to be able to also use this for ambiguous subsequences, but I'd be more than happy with help on this first question, thanks in advance!

Answer 1

I don't know if I understood You well but you can try this:
Example fasta file:
>seq1
ATGTACGTACGTACNNNNACTG
>seq2
NNNATCGTAGTCANNA
>seq3
NNNNATGNNN
Code:
from Bio import SeqIO
from Bio import SeqUtils
from Bio.Alphabet.IUPAC import ambiguous_dna
if __name__ == '__main__':
sub_seq = input('Enter a subsequence: ')
results = []
with open('test.fasta', 'r') as fh:
for seq in SeqIO.parse(fh, 'fasta', alphabet=ambiguous_dna):
if sub_seq in seq:
results.append((seq.name))
print(results, sep='\n')
Results (console):
Enter a subsequence: ATG
Results:
seq1
seq3
Enter a subsequence: NNNA
Results:
seq1
seq2
seq3