diff --git a/main/como/combine_distributions.py b/main/como/combine_distributions.py index ffca3a1c..17349afe 100644 --- a/main/como/combine_distributions.py +++ b/main/como/combine_distributions.py @@ -205,7 +205,7 @@ def _combine_z_distribution_for_context( return combined_z_matrix_df -async def _begin_combining_distributions( +def _begin_combining_distributions( context_name: str, input_matrices: InputMatrices, batch_names: BatchNames, diff --git a/main/como/merge_xomics.py b/main/como/merge_xomics.py index 0188504f..71ddd776 100644 --- a/main/como/merge_xomics.py +++ b/main/como/merge_xomics.py @@ -432,7 +432,7 @@ async def _process( if merge_zfpkm_distribution: logger.trace("Merging Z-Scores") - await _begin_combining_distributions( + _begin_combining_distributions( context_name=context_name, input_matrices=input_matrices, batch_names=batch_names, @@ -650,50 +650,42 @@ async def merge_xomics( # noqa: C901 trna_matrix: pd.DataFrame | None trna_boolean_matrix: pd.DataFrame | None trna_metadata: pd.DataFrame | None - trna_matrix, trna_boolean_matrix, trna_metadata = await asyncio.gather( - *[ - read_file(trna_matrix_or_filepath), - read_file(trna_boolean_matrix_or_filepath), - read_file(trna_metadata_filepath_or_df), - ] - ) + trna_matrix, trna_boolean_matrix, trna_metadata = await asyncio.gather(*[ + read_file(trna_matrix_or_filepath), + read_file(trna_boolean_matrix_or_filepath), + read_file(trna_metadata_filepath_or_df), + ]) # Build mrna items mrna_matrix: pd.DataFrame | None mrna_boolean_matrix: pd.DataFrame | None mrna_metadata: pd.DataFrame | None - mrna_matrix, mrna_boolean_matrix, mrna_metadata = await asyncio.gather( - *[ - read_file(mrna_matrix_or_filepath), - read_file(mrna_boolean_matrix_or_filepath), - read_file(mrna_metadata_filepath_or_df), - ] - ) + mrna_matrix, mrna_boolean_matrix, mrna_metadata = await asyncio.gather(*[ + read_file(mrna_matrix_or_filepath), + read_file(mrna_boolean_matrix_or_filepath), + read_file(mrna_metadata_filepath_or_df), + ]) # build scrna items scrna_matrix: pd.DataFrame | None scrna_boolean_matrix: pd.DataFrame | None scrna_metadata: pd.DataFrame | None - scrna_matrix, scrna_boolean_matrix, scrna_metadata = await asyncio.gather( - *[ - read_file(scrna_matrix_or_filepath), - read_file(scrna_boolean_matrix_or_filepath), - read_file(scrna_metadata_filepath_or_df), - ] - ) + scrna_matrix, scrna_boolean_matrix, scrna_metadata = await asyncio.gather(*[ + read_file(scrna_matrix_or_filepath), + read_file(scrna_boolean_matrix_or_filepath), + read_file(scrna_metadata_filepath_or_df), + ]) # build proteomic items proteomic_matrix: pd.DataFrame | None proteomic_boolean_matrix: pd.DataFrame | None proteomic_metadata: pd.DataFrame | None - proteomic_matrix, proteomic_boolean_matrix, proteomic_metadata = await asyncio.gather( - *[ - read_file(proteomic_matrix_or_filepath), - read_file(proteomic_boolean_matrix_or_filepath), - read_file(proteomic_metadata_filepath_or_df), - ] - ) + proteomic_matrix, proteomic_boolean_matrix, proteomic_metadata = await asyncio.gather(*[ + read_file(proteomic_matrix_or_filepath), + read_file(proteomic_boolean_matrix_or_filepath), + read_file(proteomic_metadata_filepath_or_df), + ]) source_weights = SourceWeights(trna=trna_weight, mrna=mrna_weight, scrna=scrna_weight, proteomics=proteomic_weight) input_matrices = InputMatrices(trna=trna_matrix, mrna=mrna_matrix, scrna=scrna_matrix, proteomics=proteomic_matrix) diff --git a/main/como/rnaseq_gen.py b/main/como/rnaseq_gen.py index 2938f0f8..ed6274ee 100644 --- a/main/como/rnaseq_gen.py +++ b/main/como/rnaseq_gen.py @@ -145,6 +145,9 @@ async def _build_count_metrics( Returns: A dataclass `ReadMatrixResults` + + Raises: + ValueError: If no columns to merge on are found, or if no sample columns are found after merging with gene information. """ matrix.dropna(subset="ensembl_gene_id", inplace=True) conversion = await ensembl_to_gene_id_and_symbol(ids=matrix["ensembl_gene_id"].tolist(), taxon=taxon)