seqwalk.filtering
=================

.. py:module:: seqwalk.filtering


Functions
---------

.. autoapisummary::

   seqwalk.filtering.rc
   seqwalk.filtering.filter_rc_3letter
   seqwalk.filtering.rc_hash_filtering
   seqwalk.filtering.filter_gc
   seqwalk.filtering.filter_pattern


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:: filter_rc_3letter(library, k)

   filter library to be RC free
   (Supplementary note X)

   :param library: list of sequences
   :param k: SSM k value

   :returns:

             filtered_library
                  list of sequences without reverse complementary k-mers
   :rtype: list of strings


.. py:function:: rc_hash_filtering(library, k)

   filter any library to be RC free, using simple hash approach
   could be slow for large libraries

   :param library: list of sequences
   :param k: SSM k value

   :returns:

             filtered_library
                  list of sequences without reverse complementary k-mers
   :rtype: list of strings


.. py:function:: filter_gc(library, gc_min, gc_max)

   filters library for sequences that have desired GC content

   :param library: list of sequences in string representation
   :param gc_min: minimum number of GC bases (int)
   :param gc_max: maximimum number of GC bases (int)

   :returns:

             filtered_library
                 list of sequences in string representation
   :rtype: list of strings


.. py:function:: filter_pattern(library, pattern)

   filters library to remove specific patterns

   :param library: list of sequences in string representation
   :param pattern: sequence pattern to be prevented

   :returns:

             filtered_library
                 list of sequences in string representation
   :rtype: list of strings