API Reference
==============

.. currentmodule:: lightmotif

.. automodule:: lightmotif

Functions
---------

.. toctree::
    :maxdepth: 1
    :hidden:
    :caption: Functions

    functions/create
    functions/stripe
    functions/scan
    functions/load

.. autosummary::
    :nosignatures:

    lightmotif.create
    lightmotif.stripe
    lightmotif.scan
    lightmotif.load

Sequence
--------

.. toctree::
    :maxdepth: 1
    :hidden:
    :caption: Sequence

    encoded
    striped

.. autosummary::
    :nosignatures:

    lightmotif.EncodedSequence
    lightmotif.StripedSequence


Matrices
--------

.. toctree::
    :maxdepth: 1
    :hidden:
    :caption: Matrices

    count
    weight
    scoring

.. autosummary::
    :nosignatures:

    lightmotif.CountMatrix
    lightmotif.WeightMatrix
    lightmotif.ScoringMatrix


Motif
-----

.. toctree::
    :maxdepth: 1
    :hidden:
    :caption: Motif

    motif/base
    motif/transfac
    motif/jaspar
    motif/uniprobe

.. autosummary::
    :nosignatures:

    lightmotif.Motif
    lightmotif.TransfacMotif
    lightmotif.JasparMotif
    lightmotif.UniprobeMotif


Scores
------

.. toctree::
    :maxdepth: 1
    :hidden:
    :caption: Scores

    scores

.. autosummary::
    :nosignatures:

    lightmotif.StripedScores


Scanner
-------

.. toctree::
    :maxdepth: 1
    :hidden:
    :caption: Scanner

    scanner

.. autosummary::
    :nosignatures:

    lightmotif.Scanner
    lightmotif.Hit


Loader
------

.. toctree::
    :maxdepth: 1
    :hidden:
    :caption: Loader

    loader

.. autosummary::
    :nosignatures:

    lightmotif.Loader