.. seq:module:: bio.seq

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

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

.. seq:class:: Kmer[k]



.. seq:class:: seq

   **Magic methods:**

      .. seq:method:: __new__(s : str)
         :noindex:

      .. seq:method:: __new__(p : Ptr[byte], l : int)
         :noindex:

      .. seq:method:: __str__()
         :noindex:

      .. seq:method:: __len__()
         :noindex:



.. seq:extension:: str

   **Magic methods:**

      .. seq:method:: __prefix_s__[N](s : str)
         :noindex:



.. seq:class:: BaseCounts

   
       Representation of base counts of a sequence
   

   **Magic methods:**

      .. seq:method:: __new__()
         :noindex:

            
                    Base counts of empty sequence (i.e. all zero)
            


      .. seq:method:: __add__(other : BaseCounts)
         :noindex:

            
                    Adds corresponding base counts
            


      .. seq:method:: __sub__(other : BaseCounts)
         :noindex:

            
                    Subtracts corresponding base counts
            


      .. seq:method:: __str__()
         :noindex:

   **Methods:**

      .. seq:method:: add(A : bool = False, C : bool = False, G : bool = False, T : bool = False, N : bool = False)

            
                    Increments the specified base counts
            




.. seq:extension:: seq

   **Properties:**

      .. seq:attribute:: bases

            
                    `BaseCount` for this sequence
            


   **Magic methods:**

      .. seq:method:: __new__(s : str)
         :noindex:

      .. seq:method:: __new__()
         :noindex:

      .. seq:method:: __eq__(other : seq)
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      .. seq:method:: __ne__(other : seq)
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      .. seq:method:: __to_py__()
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      .. seq:method:: __from_py__(s : pyobj)
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      .. seq:method:: __lt__(other : seq)
         :noindex:

      .. seq:method:: __le__(other : seq)
         :noindex:

      .. seq:method:: __gt__(other : seq)
         :noindex:

      .. seq:method:: __ge__(other : seq)
         :noindex:

      .. seq:method:: __str__()
         :noindex:

      .. seq:method:: __contains__(other : seq)
         :noindex:

      .. seq:method:: __contains__[k](kmer : Kmer[k])
         :noindex:

      .. seq:method:: __len__()
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      .. seq:method:: __bool__()
         :noindex:

      .. seq:method:: __hash__()
         :noindex:

      .. seq:method:: __getitem__(idx : int)
         :noindex:

      .. seq:method:: __getitem__(s : Slice)
         :noindex:

      .. seq:method:: __copy__()
         :noindex:

      .. seq:method:: __iter__()
         :noindex:

      .. seq:method:: __reversed__()
         :noindex:

      .. seq:method:: __int__()
         :noindex:

      .. seq:method:: __invert__()
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                    Reverse complemented sequence
            


      .. seq:method:: __reversed__()
         :noindex:

   **Methods:**

      .. seq:method:: split(k : int, step : int = 1)

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


      .. seq:method:: kmers[k](step : int = 1)

            
                    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:method:: kmers_canonical[k]()

            
                    Iterator over canonical k-mers (size `K`) of the given sequence.
                    Note that k-mers spanning ambiguous bases will be skipped.
                    A canonical k-mer is defined to be the minimum of a k-mer and
                    its reverse complement.
            


      .. seq:method:: kmers_canonical_with_pos[k]()

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


      .. seq:method:: kmers_with_pos[k](step : int = 1)

            
                    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:method:: N()

            
                    Returns whether this sequence contains ambiguous bases.
                    An ambiguous base is defined to be a non-ACGT base.
            




.. seq:extension:: seq

   **Magic methods:**

      .. seq:method:: __match__(pattern : str)
         :noindex: