cellmaps\_utils package
=======================

Description of various functions and methods provided by this package.

cellmaps\_utils.logutils module
------------------------------------

Contains methods used internally by the Cell Maps tools
to setup logging

.. automodule:: cellmaps_utils.logutils
   :members:
   :undoc-members:
   :show-inheritance:

cellmaps\_utils.provenance module
------------------------------------

Contains wrapper functionality for calls to
`FAIRSCAPE CLI <https://fairscape.github.io/fairscape-cli>`__

.. automodule:: cellmaps_utils.provenance
   :members:
   :undoc-members:
   :show-inheritance:

cellmaps\_utils.basecmdtool module
------------------------------------

Contains base class for all command line tools. Command line tools MUST subclass this

.. automodule:: cellmaps_utils.basecmdtool
   :members:
   :undoc-members:
   :show-inheritance:

cellmaps\_utils.apmstool (AP-MS) module
----------------------------------------

Contains class that creates RO-Crate of AP-MS data from raw AP-MS tables.

.. automodule:: cellmaps_utils.apmstool
   :members:
   :undoc-members:
   :show-inheritance:

cellmaps\_utils.iftool (Immunofluorescent Images) module
---------------------------------------------------------

Contains classes that download images.

.. automodule:: cellmaps_utils.iftool
   :members:
   :undoc-members:
   :show-inheritance:

cellmaps\_utils.crisprtool (CRISPR) module
-------------------------------------------

Contains class that creates RO-Crate of CRISPR data from raw CRISPR data files

.. automodule:: cellmaps_utils.crisprtool
   :members:
   :undoc-members:
   :show-inheritance:

cellmaps\_utils.tabletool (RO-Crate Table) module
--------------------------------------------------

Contains class that creates table of meta data and links from one or more RO-Crates.

.. automodule:: cellmaps_utils.tabletool
   :members:
   :undoc-members:
   :show-inheritance:

cellmaps\_utils.hidefconverter (HiDeF) module
----------------------------------------------

Contains classes that convert a hierarchy network (in CX2 format) to a HiDeF format and vice versa.

.. automodule:: cellmaps_utils.hidefconverter
   :members:
   :undoc-members:
   :show-inheritance:

cellmaps\_utils.ddotconverter (DDOT) module
----------------------------------------------

Contains classes that convert a interaction or hierarchical network (in CX2 format) to a DDOT format and vice versa.

.. automodule:: cellmaps_utils.ddotconverter
   :members:
   :undoc-members:
   :show-inheritance:

cellmaps\_utils.hcx_utils (HCX) module
----------------------------------------------

Contains classes that annotates a CX2 network with HCX annotations.

.. automodule:: cellmaps_utils.hcx_utils
   :members:
   :undoc-members:
   :show-inheritance:

cellmaps\_utils.hierdiff (Hierarchy comparison) module
----------------------------------------------------------

Contains class that compare hierarchies (Jaccard similarity)

.. automodule:: cellmaps_utils.hierdiff
   :members:
   :undoc-members:
   :show-inheritance:

cellmaps\_utils.ndexupload (NDEx upload) module
----------------------------------------------------------

Contains class that aids uploading hierarchy and interactome to NDEx

.. automodule:: cellmaps_utils.ndexupload
   :members:
   :undoc-members:
   :show-inheritance:

cellmaps\_utils.music_utils module
------------------------------------

Contains helper methods for MUSIC.

.. automodule:: cellmaps_utils.music_utils
   :members:
   :undoc-members:
   :show-inheritance:

Constants module
------------------------------------

Contains constants used by the various Cell Maps Tools

.. automodule:: cellmaps_utils.constants
   :members:
   :undoc-members:
   :show-inheritance:

Exceptions
----------

Base error classes for Cell Maps Tools

.. autoclass:: cellmaps_utils.exceptions.CellMapsError

.. autoclass:: cellmaps_utils.exceptions.CellMapsProvenanceError


Module contents
---------------

.. automodule:: cellmaps_utils
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: cellmaps_utils.cellmaps_utilscmd
   :members:
   :undoc-members:
   :show-inheritance: