mythos.input.sequence_constraints
=================================

.. py:module:: mythos.input.sequence_constraints

.. autoapi-nested-parse::

   Sequence constraint information for DNA/RNA.



Attributes
----------

.. autoapisummary::

   mythos.input.sequence_constraints.ERR_SEQ_CONSTRAINTS_INVALID_NUMBER_NUCLEOTIDES
   mythos.input.sequence_constraints.ERR_SEQ_CONSTRAINTS_INVALID_UNPAIRED_SHAPE
   mythos.input.sequence_constraints.ERR_INVALID_BP_SHAPE
   mythos.input.sequence_constraints.ERR_SEQ_CONSTRAINTS_INVALID_IS_UNPAIRED_SHAPE
   mythos.input.sequence_constraints.ERR_SEQ_CONSTRAINTS_INVALID_UNPAIRED_MAPPER_SHAPE
   mythos.input.sequence_constraints.ERR_SEQ_CONSTRAINTS_INVALID_BP_MAPPER_SHAPE
   mythos.input.sequence_constraints.ERR_SEQ_CONSTRAINTS_MISMATCH_NUM_TYPES
   mythos.input.sequence_constraints.ERR_SEQ_CONSTRAINTS_INVALID_COVER
   mythos.input.sequence_constraints.ERR_SEQ_CONSTRAINTS_IS_UNPAIRED_INVALID_VALUES
   mythos.input.sequence_constraints.ERR_SEQ_CONSTRAINTS_INVALID_IS_UNPAIRED
   mythos.input.sequence_constraints.ERR_SEQ_CONSTRAINTS_PAIRED_NT_MAPPED_TO_UNPAIRED
   mythos.input.sequence_constraints.ERR_SEQ_CONSTRAINTS_INCOMPLETE_UNPAIRED_MAPPED_IDXS
   mythos.input.sequence_constraints.ERR_SEQ_CONSTRAINTS_UNPAIRED_NT_MAPPED_TO_PAIRED
   mythos.input.sequence_constraints.ERR_SEQ_CONSTRAINTS_INCOMPLETE_BP_MAPPED_IDXS
   mythos.input.sequence_constraints.ERR_BP_ARR_CONTAINS_DUPLICATES
   mythos.input.sequence_constraints.ERR_INVALID_BP_INDICES
   mythos.input.sequence_constraints.ERR_DSEQ_TO_PSEQ_INVALID_BP


Classes
-------

.. autoapisummary::

   mythos.input.sequence_constraints.SequenceConstraints


Functions
---------

.. autoapisummary::

   mythos.input.sequence_constraints.check_consistent_constraints
   mythos.input.sequence_constraints.check_cover
   mythos.input.sequence_constraints.from_bps
   mythos.input.sequence_constraints.dseq_to_pseq


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

.. py:data:: ERR_SEQ_CONSTRAINTS_INVALID_NUMBER_NUCLEOTIDES
   :value: 'Invalid number of nucleotides'


.. py:data:: ERR_SEQ_CONSTRAINTS_INVALID_UNPAIRED_SHAPE
   :value: 'Invalid shape for unpaired nucleotides'


.. py:data:: ERR_INVALID_BP_SHAPE
   :value: 'Invalid shape for base pairs'


.. py:data:: ERR_SEQ_CONSTRAINTS_INVALID_IS_UNPAIRED_SHAPE
   :value: 'Invalid shape for array specifying if unpaired'


.. py:data:: ERR_SEQ_CONSTRAINTS_INVALID_UNPAIRED_MAPPER_SHAPE
   :value: 'Invalid shape for unpaired nucleotide index mapper'


.. py:data:: ERR_SEQ_CONSTRAINTS_INVALID_BP_MAPPER_SHAPE
   :value: 'Invalid shape for base pair index mapper'


.. py:data:: ERR_SEQ_CONSTRAINTS_MISMATCH_NUM_TYPES
   :value: 'Number of nucleotides should equal the number of unpaired base pairs plus the number of coupled...


.. py:data:: ERR_SEQ_CONSTRAINTS_INVALID_COVER
   :value: 'Unpaired and coupled nucleotides do not cover all nucleotides'


.. py:data:: ERR_SEQ_CONSTRAINTS_IS_UNPAIRED_INVALID_VALUES
   :value: 'Array specifying if unpaired contains invalid values, can only be one-hot'


.. py:data:: ERR_SEQ_CONSTRAINTS_INVALID_IS_UNPAIRED
   :value: 'Array specifying if is_unpaired disagrees with list of unpaired nucleotides'


.. py:data:: ERR_SEQ_CONSTRAINTS_PAIRED_NT_MAPPED_TO_UNPAIRED
   :value: 'Base paired nucleotides cannot be mapped to an unpaired nucleotide'


.. py:data:: ERR_SEQ_CONSTRAINTS_INCOMPLETE_UNPAIRED_MAPPED_IDXS
   :value: 'Map of position indices to indices of unpaired nucleotides does not cover number of unpaired...


.. py:data:: ERR_SEQ_CONSTRAINTS_UNPAIRED_NT_MAPPED_TO_PAIRED
   :value: 'Unpaired nucleotides cannot be mapped to a base paired nucleotide'


.. py:data:: ERR_SEQ_CONSTRAINTS_INCOMPLETE_BP_MAPPED_IDXS
   :value: 'Map of position indices to indices of base paired nucleotides does not cover number of base...


.. py:data:: ERR_BP_ARR_CONTAINS_DUPLICATES
   :value: 'Array specifying base paired indices cannot contain duplicates'


.. py:data:: ERR_INVALID_BP_INDICES
   :value: 'Base paired indices must be between 0 and n_nucleotides-1'


.. py:data:: ERR_DSEQ_TO_PSEQ_INVALID_BP
   :value: 'Invalid base pair encountered when converting discrete sequence to probabilistic sequence'


.. py:function:: check_consistent_constraints(n_unpaired: int, n_bp: int, unpaired: mythos.utils.types.Arr_Unpaired, idx_to_unpaired_idx: mythos.utils.types.Arr_Nucleotide_Int, idx_to_bp_idx: mythos.utils.types.Arr_Nucleotide_2_Int) -> None

   Checks for consistency between specified nucleotide constraints and index mappers.


.. py:function:: check_cover(n_nucleotides: int, n_unpaired: int, n_bp: int, unpaired: mythos.utils.types.Arr_Unpaired, bps: mythos.utils.types.Arr_Bp) -> None

   Checks if unpaired and paired nucleotides cover the entire set of nucleotides.


.. py:class:: SequenceConstraints

   Constraint information for a RNA/DNA strand.


   .. py:attribute:: n_nucleotides
      :type:  int


   .. py:attribute:: n_unpaired
      :type:  int


   .. py:attribute:: n_bp
      :type:  int


   .. py:attribute:: is_unpaired
      :type:  mythos.utils.types.Arr_Nucleotide_Int


   .. py:attribute:: unpaired
      :type:  mythos.utils.types.Arr_Unpaired


   .. py:attribute:: bps
      :type:  mythos.utils.types.Arr_Bp


   .. py:attribute:: idx_to_unpaired_idx
      :type:  mythos.utils.types.Arr_Nucleotide_Int


   .. py:attribute:: idx_to_bp_idx
      :type:  mythos.utils.types.Arr_Nucleotide_2_Int


   .. py:method:: __post_init__() -> None

      Check that the sequence constraints are valid.



.. py:function:: from_bps(n_nucleotides: int, bps: mythos.utils.types.Arr_Bp) -> SequenceConstraints

   Construct a SequenceConstraints object from a set of base pairs.


.. py:function:: dseq_to_pseq(dseq: mythos.utils.types.Discrete_Sequence, sc: SequenceConstraints) -> mythos.utils.types.Probabilistic_Sequence

   Converts a discrete sequence to a probabilistic sequence.