:py:mod:`deeprvat.annotations.annotations`
==========================================

.. py:module:: deeprvat.annotations.annotations

.. autodoc2-docstring:: deeprvat.annotations.annotations
   :allowtitles:

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

Functions
~~~~~~~~~

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

   * - :py:obj:`precision <deeprvat.annotations.annotations.precision>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.precision
          :summary:
   * - :py:obj:`recall <deeprvat.annotations.annotations.recall>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.recall
          :summary:
   * - :py:obj:`deepripe_get_model_info <deeprvat.annotations.annotations.deepripe_get_model_info>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.deepripe_get_model_info
          :summary:
   * - :py:obj:`seq_to_1hot <deeprvat.annotations.annotations.seq_to_1hot>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.seq_to_1hot
          :summary:
   * - :py:obj:`convert2bed <deeprvat.annotations.annotations.convert2bed>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.convert2bed
          :summary:
   * - :py:obj:`deepripe_encode_variant_bedline <deeprvat.annotations.annotations.deepripe_encode_variant_bedline>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.deepripe_encode_variant_bedline
          :summary:
   * - :py:obj:`readYamlColumns <deeprvat.annotations.annotations.readYamlColumns>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.readYamlColumns
          :summary:
   * - :py:obj:`get_parquet_columns <deeprvat.annotations.annotations.get_parquet_columns>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.get_parquet_columns
          :summary:
   * - :py:obj:`cli <deeprvat.annotations.annotations.cli>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.cli
          :summary:
   * - :py:obj:`filter_annotations_by_exon_distance <deeprvat.annotations.annotations.filter_annotations_by_exon_distance>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.filter_annotations_by_exon_distance
          :summary:
   * - :py:obj:`deepsea_pca <deeprvat.annotations.annotations.deepsea_pca>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.deepsea_pca
          :summary:
   * - :py:obj:`scorevariants_deepripe <deeprvat.annotations.annotations.scorevariants_deepripe>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.scorevariants_deepripe
          :summary:
   * - :py:obj:`process_chunk <deeprvat.annotations.annotations.process_chunk>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.process_chunk
          :summary:
   * - :py:obj:`aggregate_abscores <deeprvat.annotations.annotations.aggregate_abscores>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.aggregate_abscores
          :summary:
   * - :py:obj:`deepripe_score_variant_onlyseq_all <deeprvat.annotations.annotations.deepripe_score_variant_onlyseq_all>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.deepripe_score_variant_onlyseq_all
          :summary:
   * - :py:obj:`calculate_scores_max <deeprvat.annotations.annotations.calculate_scores_max>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.calculate_scores_max
          :summary:
   * - :py:obj:`merge_abscores <deeprvat.annotations.annotations.merge_abscores>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.merge_abscores
          :summary:
   * - :py:obj:`merge_deepripe <deeprvat.annotations.annotations.merge_deepripe>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.merge_deepripe
          :summary:
   * - :py:obj:`merge_deepsea_pcas <deeprvat.annotations.annotations.merge_deepsea_pcas>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.merge_deepsea_pcas
          :summary:
   * - :py:obj:`process_chunk_addids <deeprvat.annotations.annotations.process_chunk_addids>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.process_chunk_addids
          :summary:
   * - :py:obj:`add_ids <deeprvat.annotations.annotations.add_ids>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.add_ids
          :summary:
   * - :py:obj:`add_ids_dask <deeprvat.annotations.annotations.add_ids_dask>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.add_ids_dask
          :summary:
   * - :py:obj:`chunks <deeprvat.annotations.annotations.chunks>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.chunks
          :summary:
   * - :py:obj:`read_deepripe_file <deeprvat.annotations.annotations.read_deepripe_file>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.read_deepripe_file
          :summary:
   * - :py:obj:`concatenate_deepsea <deeprvat.annotations.annotations.concatenate_deepsea>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.concatenate_deepsea
          :summary:
   * - :py:obj:`merge_annotations <deeprvat.annotations.annotations.merge_annotations>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.merge_annotations
          :summary:
   * - :py:obj:`process_deepripe <deeprvat.annotations.annotations.process_deepripe>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.process_deepripe
          :summary:
   * - :py:obj:`process_vep <deeprvat.annotations.annotations.process_vep>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.process_vep
          :summary:
   * - :py:obj:`compute_plof <deeprvat.annotations.annotations.compute_plof>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.compute_plof
          :summary:
   * - :py:obj:`concat_annotations <deeprvat.annotations.annotations.concat_annotations>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.concat_annotations
          :summary:
   * - :py:obj:`get_af_from_gt <deeprvat.annotations.annotations.get_af_from_gt>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.get_af_from_gt
          :summary:
   * - :py:obj:`merge_af <deeprvat.annotations.annotations.merge_af>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.merge_af
          :summary:
   * - :py:obj:`calculate_maf <deeprvat.annotations.annotations.calculate_maf>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.calculate_maf
          :summary:
   * - :py:obj:`add_gene_ids <deeprvat.annotations.annotations.add_gene_ids>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.add_gene_ids
          :summary:
   * - :py:obj:`create_gene_id_file <deeprvat.annotations.annotations.create_gene_id_file>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.create_gene_id_file
          :summary:
   * - :py:obj:`select_rename_fill_annotations <deeprvat.annotations.annotations.select_rename_fill_annotations>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.select_rename_fill_annotations
          :summary:
   * - :py:obj:`aggregate_and_concat_absplice <deeprvat.annotations.annotations.aggregate_and_concat_absplice>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.aggregate_and_concat_absplice
          :summary:
   * - :py:obj:`merge_absplice_scores <deeprvat.annotations.annotations.merge_absplice_scores>`
     - .. autodoc2-docstring:: deeprvat.annotations.annotations.merge_absplice_scores
          :summary:

Data
~~~~

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

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

API
~~~

.. py:function:: precision(y_true, y_pred)
   :canonical: deeprvat.annotations.annotations.precision

   .. autodoc2-docstring:: deeprvat.annotations.annotations.precision

.. py:function:: recall(y_true, y_pred)
   :canonical: deeprvat.annotations.annotations.recall

   .. autodoc2-docstring:: deeprvat.annotations.annotations.recall

.. py:function:: deepripe_get_model_info(saved_models_dict, saved_deepripe_models_path)
   :canonical: deeprvat.annotations.annotations.deepripe_get_model_info

   .. autodoc2-docstring:: deeprvat.annotations.annotations.deepripe_get_model_info

.. py:function:: seq_to_1hot(seq, randomsel=True)
   :canonical: deeprvat.annotations.annotations.seq_to_1hot

   .. autodoc2-docstring:: deeprvat.annotations.annotations.seq_to_1hot

.. py:function:: convert2bed(variants_file, output_dir)
   :canonical: deeprvat.annotations.annotations.convert2bed

   .. autodoc2-docstring:: deeprvat.annotations.annotations.convert2bed

.. py:function:: deepripe_encode_variant_bedline(bedline, genomefasta, flank_size=75)
   :canonical: deeprvat.annotations.annotations.deepripe_encode_variant_bedline

   .. autodoc2-docstring:: deeprvat.annotations.annotations.deepripe_encode_variant_bedline

.. py:function:: readYamlColumns(annotation_columns_yaml_file)
   :canonical: deeprvat.annotations.annotations.readYamlColumns

   .. autodoc2-docstring:: deeprvat.annotations.annotations.readYamlColumns

.. py:function:: get_parquet_columns(parquet_file)
   :canonical: deeprvat.annotations.annotations.get_parquet_columns

   .. autodoc2-docstring:: deeprvat.annotations.annotations.get_parquet_columns

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

   .. autodoc2-docstring:: deeprvat.annotations.annotations.cli

.. py:function:: filter_annotations_by_exon_distance(anno_path: str, gtf_path: str, genes_path: str, output_path: str, max_dist: int) -> None
   :canonical: deeprvat.annotations.annotations.filter_annotations_by_exon_distance

   .. autodoc2-docstring:: deeprvat.annotations.annotations.filter_annotations_by_exon_distance

.. py:function:: deepsea_pca(deepsea_file: str, pca_object: str, means_sd_df: str, out_dir: str, n_components: int)
   :canonical: deeprvat.annotations.annotations.deepsea_pca

   .. autodoc2-docstring:: deeprvat.annotations.annotations.deepsea_pca

.. py:function:: scorevariants_deepripe(variants_file: str, output_dir: str, genomefasta: str, pybedtools_tmp_dir: str, saved_deepripe_models_path: str, n_jobs: int, saved_model_type: str = 'parclip')
   :canonical: deeprvat.annotations.annotations.scorevariants_deepripe

   .. autodoc2-docstring:: deeprvat.annotations.annotations.scorevariants_deepripe

.. py:function:: process_chunk(chrom_file, abs_splice_res_dir, tissues_to_exclude, tissue_agg_function, ca_shortened)
   :canonical: deeprvat.annotations.annotations.process_chunk

   .. autodoc2-docstring:: deeprvat.annotations.annotations.process_chunk

.. py:function:: aggregate_abscores(current_annotation_file: str, abs_splice_res_dir: str, absplice_score_file: str, njobs: int)
   :canonical: deeprvat.annotations.annotations.aggregate_abscores

   .. autodoc2-docstring:: deeprvat.annotations.annotations.aggregate_abscores

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

   .. autodoc2-docstring:: deeprvat.annotations.annotations.logger

.. py:function:: deepripe_score_variant_onlyseq_all(model_group, variant_bed, genomefasta, seq_len=200, batch_size=1024, n_jobs=32)
   :canonical: deeprvat.annotations.annotations.deepripe_score_variant_onlyseq_all

   .. autodoc2-docstring:: deeprvat.annotations.annotations.deepripe_score_variant_onlyseq_all

.. py:function:: calculate_scores_max(scores)
   :canonical: deeprvat.annotations.annotations.calculate_scores_max

   .. autodoc2-docstring:: deeprvat.annotations.annotations.calculate_scores_max

.. py:function:: merge_abscores(current_annotation_file: str, absplice_score_file: str, out_file: str)
   :canonical: deeprvat.annotations.annotations.merge_abscores

   .. autodoc2-docstring:: deeprvat.annotations.annotations.merge_abscores

.. py:function:: merge_deepripe(annotation_file: str, deepripe_file: str, out_file: str, column_prefix: str)
   :canonical: deeprvat.annotations.annotations.merge_deepripe

   .. autodoc2-docstring:: deeprvat.annotations.annotations.merge_deepripe

.. py:function:: merge_deepsea_pcas(annotation_file: str, deepripe_pca_file: str, column_yaml_file: str, out_file: str)
   :canonical: deeprvat.annotations.annotations.merge_deepsea_pcas

   .. autodoc2-docstring:: deeprvat.annotations.annotations.merge_deepsea_pcas

.. py:function:: process_chunk_addids(chunk: pandas.DataFrame, variants: pandas.DataFrame) -> pandas.DataFrame
   :canonical: deeprvat.annotations.annotations.process_chunk_addids

   .. autodoc2-docstring:: deeprvat.annotations.annotations.process_chunk_addids

.. py:function:: add_ids(annotation_file: str, variant_file: str, njobs: int, out_file: str)
   :canonical: deeprvat.annotations.annotations.add_ids

   .. autodoc2-docstring:: deeprvat.annotations.annotations.add_ids

.. py:function:: add_ids_dask(annotation_file: str, variant_file: str, out_file: str)
   :canonical: deeprvat.annotations.annotations.add_ids_dask

   .. autodoc2-docstring:: deeprvat.annotations.annotations.add_ids_dask

.. py:function:: chunks(lst, n)
   :canonical: deeprvat.annotations.annotations.chunks

   .. autodoc2-docstring:: deeprvat.annotations.annotations.chunks

.. py:function:: read_deepripe_file(f: str)
   :canonical: deeprvat.annotations.annotations.read_deepripe_file

   .. autodoc2-docstring:: deeprvat.annotations.annotations.read_deepripe_file

.. py:function:: concatenate_deepsea(deepsea_files: str, out_file: str, njobs: int)
   :canonical: deeprvat.annotations.annotations.concatenate_deepsea

   .. autodoc2-docstring:: deeprvat.annotations.annotations.concatenate_deepsea

.. py:function:: merge_annotations(vep_header_line: int, vep_file: str, deepripe_parclip_file: str, deepripe_hg2_file: str, deepripe_k5_file: str, variant_file: str, vcf_file: str, out_file: str, column_yaml: str)
   :canonical: deeprvat.annotations.annotations.merge_annotations

   .. autodoc2-docstring:: deeprvat.annotations.annotations.merge_annotations

.. py:function:: process_deepripe(deepripe_df: pandas.DataFrame, column_prefix: str) -> pandas.DataFrame
   :canonical: deeprvat.annotations.annotations.process_deepripe

   .. autodoc2-docstring:: deeprvat.annotations.annotations.process_deepripe

.. py:function:: process_vep(vep_file: pandas.DataFrame, vcf_file: str, types_mapping: dict) -> pandas.DataFrame
   :canonical: deeprvat.annotations.annotations.process_vep

   .. autodoc2-docstring:: deeprvat.annotations.annotations.process_vep

.. py:function:: compute_plof(anno_df_in, anno_df_out)
   :canonical: deeprvat.annotations.annotations.compute_plof

   .. autodoc2-docstring:: deeprvat.annotations.annotations.compute_plof

.. py:function:: concat_annotations(filenames: str, out_file: str)
   :canonical: deeprvat.annotations.annotations.concat_annotations

   .. autodoc2-docstring:: deeprvat.annotations.annotations.concat_annotations

.. py:function:: get_af_from_gt(genotype_file: str, variants_filepath: str, out_file: str)
   :canonical: deeprvat.annotations.annotations.get_af_from_gt

   .. autodoc2-docstring:: deeprvat.annotations.annotations.get_af_from_gt

.. py:function:: merge_af(annotations_path: str, af_df_path: str, out_file: str)
   :canonical: deeprvat.annotations.annotations.merge_af

   .. autodoc2-docstring:: deeprvat.annotations.annotations.merge_af

.. py:function:: calculate_maf(annotations_path: str, out_file: str, af_column_name: str)
   :canonical: deeprvat.annotations.annotations.calculate_maf

   .. autodoc2-docstring:: deeprvat.annotations.annotations.calculate_maf

.. py:function:: add_gene_ids(gene_id_file: str, annotations_path: str, out_file: str)
   :canonical: deeprvat.annotations.annotations.add_gene_ids

   .. autodoc2-docstring:: deeprvat.annotations.annotations.add_gene_ids

.. py:function:: create_gene_id_file(gtf_filepath: str, out_file: str)
   :canonical: deeprvat.annotations.annotations.create_gene_id_file

   .. autodoc2-docstring:: deeprvat.annotations.annotations.create_gene_id_file

.. py:function:: select_rename_fill_annotations(annotation_columns_yaml_file: str, annotations_path: str, out_file: str, keep_unfilled: str)
   :canonical: deeprvat.annotations.annotations.select_rename_fill_annotations

   .. autodoc2-docstring:: deeprvat.annotations.annotations.select_rename_fill_annotations

.. py:function:: aggregate_and_concat_absplice(absplice_dir: str, ab_splice_agg_score_file: str) -> None
   :canonical: deeprvat.annotations.annotations.aggregate_and_concat_absplice

   .. autodoc2-docstring:: deeprvat.annotations.annotations.aggregate_and_concat_absplice

.. py:function:: merge_absplice_scores(annotations, variants, genes, ab_splice_agg_score_file, output, verbose, mem_limit, fill_nan)
   :canonical: deeprvat.annotations.annotations.merge_absplice_scores

   .. autodoc2-docstring:: deeprvat.annotations.annotations.merge_absplice_scores