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Clinvar-build documentation
===========================

Clinvar-build is a Python packages which allows the user to 
create a custom SQLite database using the publicly available
XML files updated weekly by ClinVar.

The latest version of the XML files can be obtained from their public FTP:
`server <https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xsd_public/>`_.
These files contain both VCV (Variation ClinVar) and RCV (Reference ClinVar) records.
The VCV represents the aggregate record for a single genetic variant across all
submissions. The RCV captures condition-specific interpretations for that variant and
aggregates the corresponding SCV records, which represent individual submissions to
ClinVar.

The package is designed to allow the user full control about which 
information they want to extract, encoding the schema structure in 
TOML like `.cnf` files and the parsing instruction (based on Xpaths) 
in `.json` files. 

Installation
------------

The package can be installed from `GitLab <https://gitlab.com/SchmidtAF/clinvar-build>`_.

ClinVar documentation
---------------------

Please refer to ClinVar's detailed `documentation <https://www.ncbi.nlm.nih.gov/projects/clinvar/ClinVarDataDictionary.pdf>`_.
for an overview of the XML content. 
Additionally refer to the XSD files which can be use to validate the XML files. 
The XSD files used to build the current version of the module are included 
`here <https://gitlab.com/SchmidtAF/clinvar-build/-/tree/master/resources/clinvar_config/xsd?ref_type=heads>`_.

Documentation
=============

.. toctree::
   :maxdepth: 1
   :caption: Quick start 

   quickstart
   environment
   schema_config
   parser_config


.. toctree::
   :maxdepth: 1
   :caption: Examples

   .. examples/plots/barcharts.nblink
   .. examples/plots/forestplot.nblink
   .. examples/plots/heatmap.nblink
   .. examples/plots/incidencematrix.nblink
   .. examples/plots/machine_learning.nblink
   .. examples/plots/pychart.nblink
   .. examples/plots/survival.nblink
   .. examples/plots/volcanoplot.nblink


.. toctree::
   :maxdepth: 1
   :caption: Additional documentation

   api


.. toctree::
   :maxdepth: 1
   :caption: Project admin

   contributing
   raising_issues


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`