cnvlib package
==============

Module ``cnvlib`` contents
--------------------------

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The one function exposed at the top level, `read`, loads a file in CNVkit's
BED-like tabular format and returns a CopyNumArray instance. For your own
scripting, you can usually accomplish what you need using just the CopyNumArray
and GenomicArray methods available on this returned object (see
:ref:`api_classes`).

To load other file formats, see :ref:`api_tabio`. To run functions equivalent to
CNVkit commands within Python, see :ref:`api_commands`.


.. _api_classes:

Core classes
------------

The core objects used throughout CNVkit. The base class is GenomicArray from
:doc:`skgenome`. All of these classes wrap a `pandas
<http://pandas.pydata.org/>`_ DataFrame instance, which is accessible through
the ``.data`` attribute and can be used for any manipulations that aren't
already provided by methods in the wrapper class.

``cnary``
~~~~~~~~~

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``vary``
~~~~~~~~

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.. _api_commands:

Interface to CNVkit sub-commands
--------------------------------

``commands``
~~~~~~~~~~~~

The public API for each of the commands defined in the CNVkit workflow.

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The following modules implement lower-level functionality specific to each of
the CNVkit sub-commands.

``access``
~~~~~~~~~~

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``antitarget``
~~~~~~~~~~~~~~

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``autobin``
~~~~~~~~~~~

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``batch``
~~~~~~~~~

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``call``
~~~~~~~~

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``coverage``
~~~~~~~~~~~~

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``diagram``
~~~~~~~~~~~

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``export``
~~~~~~~~~~

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``fix``
~~~~~~~

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``heatmap``
~~~~~~~~~~~

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``importers``
~~~~~~~~~~~~~

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``import_rna``
~~~~~~~~~~~~~~

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``metrics``
~~~~~~~~~~~

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``reference``
~~~~~~~~~~~~~

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``reports``
~~~~~~~~~~~

Supports the sub-commands :ref:`breaks` and :ref:`genemetrics`.

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``scatter``
~~~~~~~~~~~

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``segmentation``
~~~~~~~~~~~~~~~~

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``segmetrics``
~~~~~~~~~~~~~~~~

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``target``
~~~~~~~~~~

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.. _api_helpers:

Helper modules
--------------

``cmdutil``
~~~~~~~~~~~

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``core``
~~~~~~~~

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``descriptives``
~~~~~~~~~~~~~~~~

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``parallel``
~~~~~~~~~~~~

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``params``
~~~~~~~~~~

Defines several constants used in the pipeline.

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``plots``
~~~~~~~~~

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``rna``
~~~~~~~~~

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``samutil``
~~~~~~~~~~~

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``segfilters``
~~~~~~~~~~~~~~

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``smoothing``
~~~~~~~~~~~~~

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