:py:mod:`deeprvat.deeprvat.common_variant_condition_utils`
==========================================================

.. py:module:: deeprvat.deeprvat.common_variant_condition_utils

.. autodoc2-docstring:: deeprvat.deeprvat.common_variant_condition_utils
   :allowtitles:

Module Contents
---------------

Functions
~~~~~~~~~

.. list-table::
   :class: autosummary longtable
   :align: left

   * - :py:obj:`cli <deeprvat.deeprvat.common_variant_condition_utils.cli>`
     - .. autodoc2-docstring:: deeprvat.deeprvat.common_variant_condition_utils.cli
          :summary:
   * - :py:obj:`get_significant_genes <deeprvat.deeprvat.common_variant_condition_utils.get_significant_genes>`
     - .. autodoc2-docstring:: deeprvat.deeprvat.common_variant_condition_utils.get_significant_genes
          :summary:
   * - :py:obj:`prepare_genotypes_per_gene <deeprvat.deeprvat.common_variant_condition_utils.prepare_genotypes_per_gene>`
     - .. autodoc2-docstring:: deeprvat.deeprvat.common_variant_condition_utils.prepare_genotypes_per_gene
          :summary:

Data
~~~~

.. list-table::
   :class: autosummary longtable
   :align: left

   * - :py:obj:`compression_level <deeprvat.deeprvat.common_variant_condition_utils.compression_level>`
     - .. autodoc2-docstring:: deeprvat.deeprvat.common_variant_condition_utils.compression_level
          :summary:
   * - :py:obj:`logger <deeprvat.deeprvat.common_variant_condition_utils.logger>`
     - .. autodoc2-docstring:: deeprvat.deeprvat.common_variant_condition_utils.logger
          :summary:

API
~~~

.. py:data:: compression_level
   :canonical: deeprvat.deeprvat.common_variant_condition_utils.compression_level
   :value: 1

   .. autodoc2-docstring:: deeprvat.deeprvat.common_variant_condition_utils.compression_level

.. py:data:: logger
   :canonical: deeprvat.deeprvat.common_variant_condition_utils.logger
   :value: 'getLogger(...)'

   .. autodoc2-docstring:: deeprvat.deeprvat.common_variant_condition_utils.logger

.. py:function:: cli()
   :canonical: deeprvat.deeprvat.common_variant_condition_utils.cli

   .. autodoc2-docstring:: deeprvat.deeprvat.common_variant_condition_utils.cli

.. py:function:: get_significant_genes(alpha, pval_correction_method, debug, config_file, res_file, out_parquet, out_gene_ids)
   :canonical: deeprvat.deeprvat.common_variant_condition_utils.get_significant_genes

   .. autodoc2-docstring:: deeprvat.deeprvat.common_variant_condition_utils.get_significant_genes

.. py:function:: prepare_genotypes_per_gene(standardize: bool, gtf_file: str, padding: int, sample_file: str, sig_gene_file: str, genotype_file, config_file: str, out_dir: str)
   :canonical: deeprvat.deeprvat.common_variant_condition_utils.prepare_genotypes_per_gene

   .. autodoc2-docstring:: deeprvat.deeprvat.common_variant_condition_utils.prepare_genotypes_per_gene