bio.builtin¶
Source code: bio/builtin.seq
- bio.builtin.prefetch()¶
- bio.builtin.inter_align()¶
- 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 (size 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 equal to K but with the base at index idx set to b