Exemplos de find_kmers em Python

Exemplo n.º 1

Arquivo: solution3_revp.py Projeto: sunilnahata/biofx_python

def revp(seq: str, k: int) -> List[int]:
    """ Return positions of reverse palindromes """

    kmers = find_kmers(seq, k)
    revc = map(Seq.reverse_complement, kmers)
    pairs = enumerate(zip(kmers, revc))
    return [pos + 1 for pos, pair in pairs if operator.eq(*pair)]

Exemplo n.º 2

def main() -> None:
    """ Make a jazz noise here """

    args = get_args()
    for rec in SeqIO.parse(args.file, 'fasta'):
        for k in range(4, 13):
            kmers = find_kmers(str(rec.seq), k)
            revc = list(map(Seq.reverse_complement, kmers))

            for pos, pair in enumerate(zip(kmers, revc)):
                if operator.eq(*pair):
                    print(pos + 1, k)

Exemplo n.º 3

Arquivo: solution2_operator_eq_lc.py Projeto: sunilnahata/biofx_python

def main() -> None:
    """ Make a jazz noise here """

    args = get_args()
    if seqs := [str(rec.seq) for rec in SeqIO.parse(args.file, 'fasta')]:
        seq = seqs[0]

        for k in range(4, 13):
            kmers = find_kmers(seq, k)
            revc = map(Seq.reverse_complement, kmers)
            pairs = enumerate(zip(kmers, revc))

            for pos in [pos + 1 for pos, pair in pairs if operator.eq(*pair)]:
                print(pos, k)

Exemplo n.º 4

Arquivo: solution1_zip_enumerate.py Projeto: MarcBanuls/biofx_python

def main() -> None:
    """ Make a jazz noise here """

    args = get_args()
    if seqs := [str(rec.seq) for rec in SeqIO.parse(args.file, 'fasta')]:
        seq = seqs[0]

        for k in range(4, 13):
            kmers = find_kmers(seq, k)
            revc = list(map(Seq.reverse_complement, kmers))

            for pos, pair in enumerate(zip(kmers, revc)):
                if fst(pair) == snd(pair):
                    print(pos + 1, k)