bio.builtin

Source code: bio/builtin.seq

bio.builtin.seqs(x)

Returns an iterator over sequences from the specified object by invoking the __seqs__ magic method.

__seqs__ is defined for most common formats, like FASTA, FASTQ, SAM and BAM.

bio.builtin.split(self: seq, k: int, step: int)

Iterator over length-k subsequences of the given sequence with the specified step size.

bio.builtin.kmers[K](self: seq, step: int)

Iterator over k-mers (type K) of the given sequence with the specified step size. Note that k-mers spanning ambiguous bases will be skipped.

bio.builtin.kmers_with_pos[K](self: seq, step: int)

Iterator over (0-based index, k-mer) tuples of the given sequence with the specified step size. Note that k-mers spanning ambiguous bases will be skipped.

bio.builtin.revcomp(s)

Returns the reverse complement of the argument sequence or k-mer.

bio.builtin.revcomp_with_pos(t)

Returns the reverse complement of the argument sequence or k-mer, where the argument also contains a position (e.g. as yielded by kmers_with_pos).

bio.builtin.canonical(k)

Returns the minimum of a sequence / k-mer and its reverse complement.

bio.builtin.canonical_with_pos(t)

Returns the minimum of a sequence / k-mer and its reverse complement, where the argument also contains a position (e.g. as yielded by kmers_with_pos).

bio.builtin.base[K, T](kmer: K, idx: int, b: T)

Returns a new k-mer based on kmer with the base at idx replaced with b.