:py:mod:`deeprvat.preprocessing.preprocess`
===========================================

.. py:module:: deeprvat.preprocessing.preprocess

.. autodoc2-docstring:: deeprvat.preprocessing.preprocess
   :allowtitles:

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

Functions
~~~~~~~~~

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

   * - :py:obj:`drop_rows <deeprvat.preprocessing.preprocess.drop_rows>`
     - .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.drop_rows
          :summary:
   * - :py:obj:`ragged_to_matrix <deeprvat.preprocessing.preprocess.ragged_to_matrix>`
     - .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.ragged_to_matrix
          :summary:
   * - :py:obj:`process_sparse_gt_file <deeprvat.preprocessing.preprocess.process_sparse_gt_file>`
     - .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.process_sparse_gt_file
          :summary:
   * - :py:obj:`postprocess_sparse_gt <deeprvat.preprocessing.preprocess.postprocess_sparse_gt>`
     - .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.postprocess_sparse_gt
          :summary:
   * - :py:obj:`write_genotype_file <deeprvat.preprocessing.preprocess.write_genotype_file>`
     - .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.write_genotype_file
          :summary:
   * - :py:obj:`cli <deeprvat.preprocessing.preprocess.cli>`
     - .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.cli
          :summary:
   * - :py:obj:`add_variant_ids <deeprvat.preprocessing.preprocess.add_variant_ids>`
     - .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.add_variant_ids
          :summary:
   * - :py:obj:`get_file_chromosome <deeprvat.preprocessing.preprocess.get_file_chromosome>`
     - .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.get_file_chromosome
          :summary:
   * - :py:obj:`parse_file_path_list <deeprvat.preprocessing.preprocess.parse_file_path_list>`
     - .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.parse_file_path_list
          :summary:
   * - :py:obj:`process_individual_missingness <deeprvat.preprocessing.preprocess.process_individual_missingness>`
     - .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.process_individual_missingness
          :summary:
   * - :py:obj:`process_sparse_gt <deeprvat.preprocessing.preprocess.process_sparse_gt>`
     - .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.process_sparse_gt
          :summary:
   * - :py:obj:`combine_genotypes <deeprvat.preprocessing.preprocess.combine_genotypes>`
     - .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.combine_genotypes
          :summary:

Data
~~~~

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

   * - :py:obj:`logger <deeprvat.preprocessing.preprocess.logger>`
     - .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.logger
          :summary:

API
~~~

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

   .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.logger

.. py:function:: drop_rows(df: pandas.DataFrame, df_to_drop: pandas.DataFrame) -> pandas.DataFrame
   :canonical: deeprvat.preprocessing.preprocess.drop_rows

   .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.drop_rows

.. py:function:: ragged_to_matrix(rows: typing.List[numpy.ndarray], pad_value: int = -1, max_len: typing.Optional[int] = None) -> numpy.ndarray
   :canonical: deeprvat.preprocessing.preprocess.ragged_to_matrix

   .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.ragged_to_matrix

.. py:function:: process_sparse_gt_file(file: str, variants: pandas.DataFrame, samples: typing.List[str], calls_to_exclude: pandas.DataFrame = None) -> typing.Tuple[typing.List[numpy.ndarray], typing.List[numpy.ndarray]]
   :canonical: deeprvat.preprocessing.preprocess.process_sparse_gt_file

   .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.process_sparse_gt_file

.. py:function:: postprocess_sparse_gt(processed: typing.List[typing.Tuple[typing.List[numpy.ndarray], typing.List[numpy.ndarray]]], result_index: int, n_rows: int) -> numpy.ndarray
   :canonical: deeprvat.preprocessing.preprocess.postprocess_sparse_gt

   .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.postprocess_sparse_gt

.. py:function:: write_genotype_file(f: h5py.File, samples: numpy.ndarray, variant_matrix: numpy.ndarray, genotype_matrix: numpy.ndarray, count_variants: typing.Optional[numpy.ndarray] = None)
   :canonical: deeprvat.preprocessing.preprocess.write_genotype_file

   .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.write_genotype_file

.. py:function:: cli()
   :canonical: deeprvat.preprocessing.preprocess.cli

   .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.cli

.. py:function:: add_variant_ids(variant_file: str, out_file: str, duplicates_file: str, chromosomes: typing.Optional[str] = None)
   :canonical: deeprvat.preprocessing.preprocess.add_variant_ids

   .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.add_variant_ids

.. py:function:: get_file_chromosome(file, col_names, chrom_field='chrom')
   :canonical: deeprvat.preprocessing.preprocess.get_file_chromosome

   .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.get_file_chromosome

.. py:function:: parse_file_path_list(file_path_list_path: pathlib.Path)
   :canonical: deeprvat.preprocessing.preprocess.parse_file_path_list

   .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.parse_file_path_list

.. py:function:: process_individual_missingness(threshold: float, file_paths_list: pathlib.Path, imiss_dir: str, out_file: str)
   :canonical: deeprvat.preprocessing.preprocess.process_individual_missingness

   .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.process_individual_missingness

.. py:function:: process_sparse_gt(chunksize: int, exclude_variants: typing.List[str], exclude_samples: typing.Optional[str], exclude_calls: typing.Optional[str], chromosomes: typing.Optional[str], skip_sanity_checks: bool, variant_file: str, samples_path: str, sparse_gt: str, out_file: str)
   :canonical: deeprvat.preprocessing.preprocess.process_sparse_gt

   .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.process_sparse_gt

.. py:function:: combine_genotypes(chunksize: typing.Optional[int], genotype_files: typing.List[str], out_file: str)
   :canonical: deeprvat.preprocessing.preprocess.combine_genotypes

   .. autodoc2-docstring:: deeprvat.preprocessing.preprocess.combine_genotypes