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Python API

This page provides detailed documentation for the pyslim Python API.

Additions to the tree sequence

The :class:`tskit.TreeSequence` class represents a sequence of correlated trees that describes the genealogical history of a population. Here, we describe pyslim's additions to this class.

The SLiM Tree Sequence

.. autoclass:: pyslim.SlimTreeSequence()
    :members:

Constants

.. data:: slim_tree_sequence.py:NUCLEOTIDES == ['A', 'C', 'G', 'T']

   Nucleotide states in nucleotide models are encoded as integers (0, 1, 2, 3);
   this gives the mapping.

These constants are used to encode the "genome type" of a Node.

.. data:: GENOME_TYPE_AUTOSOME == 0


.. data:: GENOME_TYPE_X == 1


.. data:: GENOME_TYPE_Y == 2

These constants are used to encode other information about Individuals.

.. data:: INDIVIDUAL_TYPE_HERMAPHRODITE == -1


.. data:: INDIVIDUAL_TYPE_FEMALE == 0


.. data:: INDIVIDUAL_TYPE_MALE == 1


.. data:: INDIVIDUAL_FLAG_MIGRATED == 0x01

And, these are used in the Individual.flags:

.. data:: INDIVIDUAL_ALIVE == 2**16

   This flag is used by SLiM to record information in the :class:`tskit.Individual` metadata.


.. data:: INDIVIDUAL_REMEMBERED == 2**17

   This flag is used by SLiM to record information in the :class:`tskit.Individual` metadata.


.. data:: INDIVIDUAL_RETAINED == 2**18

   This flag is used by SLiM to record information in the :class:`tskit.Individual` metadata.

Metadata

SLiM-specific metadata is made visible to the user by .metadata properties. For instance:

>>> ts.node(3).metadata
{"slim_id" : 3, "is_null" : 0, "genome_type" : 0}

shows that the fourth node in the tree sequence was given pedigree ID 3 by SLiM, is not a null genome, and has genome_type zero, which corresponds to an autosome (see below).

Annotation

These two functions will add default SLiM metadata to a tree sequence (or the underlying tables), which can then be modified and loaded into SLiM.

.. autofunction:: pyslim.annotate_defaults


.. autofunction:: pyslim.annotate_defaults_tables

Provenances

.. autoclass:: pyslim.ProvenanceMetadata
   :members:


.. autofunction:: pyslim.get_provenance