seqwalk.generation
==================

.. py:module:: seqwalk.generation


Functions
---------

.. autoapisummary::

   seqwalk.generation.rc
   seqwalk.generation.partition_path
   seqwalk.generation.is_necklace
   seqwalk.generation.f
   seqwalk.generation.simple_shift
   seqwalk.generation.out_edges
   seqwalk.generation.adapted_hierholzer


Module Contents
---------------

.. py:function:: rc(seq)

   reverse complement of DNA sequence

   :param seq: string with letters in {A, C, G, T}

   :returns: string corresponding to reverse complement


.. py:function:: partition_path(seq, L, k)

   partitions self-avoiding walk into appropriate length sequences

   :param seq: self avoiding walk (string or list)
   :param L: length of desired sequences
   :param k: SSM k-value

   :returns: list of strings, each a length L seq
   :rtype: seqs


.. py:function:: is_necklace(seq)

   computes if a sequence is a necklace (as defined in Wong 2017)

   :param seq: typically list of ints


.. py:function:: f(seq, k)

   helper function defined in Wong 2017
   * note confusing notation switch

   :param seq: list of ints
   :param k: alphabet length

   :returns: int corresponding to next element of seq


.. py:function:: simple_shift(n, k)

   simple shift rule from Wong 2017
   * note confusing notation switch

   :param n: SSM k value
   :param k: alphabet size

   :returns: list of integers corresponding to H. path


.. py:function:: out_edges(v, alphabet)

   lists outedges for a node in a kmer graph

   :param v: string corresponding to node
   :param alphabet: string containing all valid letters

   :returns: list of outedges represented as strings


.. py:function:: adapted_hierholzer(k, alphabet)

   finds RC-free path through 4-letter kmer graph using modified hierholzer
   (see Supplementary Note X)

   :param k: SSM k (integer)
   :param alphabet: string containing all valid letters

   :returns: string corresponding to RC-free self-avoiding walk
   :rtype: path