seqwalk.design
==============

.. py:module:: seqwalk.design


Functions
---------

.. autoapisummary::

   seqwalk.design.max_size
   seqwalk.design.max_orthogonality


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

.. py:function:: max_size(L, k, alphabet='ACT', RCfree=False, GClims=None, prevented_patterns=['AAAA', 'CCCC', 'GGGG', 'TTTT'], verbose=True)

   design a max size library of length L sequences with SSM k

   :param L: integer length of desired seqs
   :param k: SSM k value
   :param alphabet: string of allowable letters (default "ACT")
   :param RCfree: bool, True if orthogonality with RCs is required
   :param GClims: tuple of (GCmin, GCmax), allowable range of number of GC bases
   :param prevented_patterns: list of prevented patterns (default 4N)
   :param verbose: bool, True if print and warning statements are desired

   :returns:

             seqs
                 library of orthogonal sequences
   :rtype: list of strings


.. py:function:: max_orthogonality(N, L, alphabet='ACT', RCfree=False, GClims=None, prevented_patterns=['AAAA', 'CCCC', 'GGGG', 'TTTT'], k_init=None, verbose=True)

   design a maximally orthogonal library of N length L sequences

   :param N: minimum number of sequences in library
   :param L: integer length of desired seqs
   :param alphabet: string of allowable letters (default "ACT")
   :param RCfree: bool, True if orthogonality with RCs is required
   :param GClims: tuple of (GCmin, GCmax), allowable range of number of GC bases
   :param prevented_patterns: list of prevented patterns (default 4N)
   :param k_init: initial guess for SSM k value
   :param verbose: bool, True if print and warning statements are desired

   :returns:

             seqs
                 library of orthogonal sequences
   :rtype: list of strings