.. seq:module:: bio.builtin

:seq:mod:`bio.builtin`
----------------------

Source code: `bio/builtin.seq <https://github.com/seq-lang/seq/blob/master/stdlib/bio/builtin.seq>`_

.. seq:function:: prefetch()



.. seq:function:: inter_align()



.. seq:function:: 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.
   



.. seq:function:: split(self : seq, k : int, step : int)

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



.. seq:function:: 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.
   



.. seq:function:: 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.
   



.. seq:function:: revcomp(s)

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



.. seq:function:: 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`).
   



.. seq:function:: canonical(k)

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



.. seq:function:: 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`).
   



.. seq:function:: 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`