marvel API

This section documents the MARVELous Python API for programmatic usage.

• marvel.pipeline module
  • Main Pipeline
    • MARVELousPipeline
      • MARVELousPipeline.from_config_file()
      • MARVELousPipeline.get_summary()
      • MARVELousPipeline.run()
  • Pipeline Steps
    • Abstract Base Class
      • PipelineStep
    • Variant Extraction Step
      • VariantExtractionStep
    • Association Testing Step
      • AssociationTestingStep
  • Entry Point
    • main()
    • marvelous()
• marvel.association package
  • marvel.association.class_test module
    • AssociationResult
      • AssociationResult.baseline_table
      • AssociationResult.coefficient_table
    • BaselineTestWrapper
      • BaselineTestWrapper.run_single_test()
    • DataValidator
      • DataValidator.check_sample_size()
      • DataValidator.check_stratified_variation()
      • DataValidator.check_string_columns()
    • DifferencesTester
      • DifferencesTester.run()
    • InsufficientVariationError
    • ModelComparator
      • ModelComparator.run()
    • OutcomeCategoryTester
      • OutcomeCategoryTester.run()
    • TestTypeResolver
      • TestTypeResolver.resolve()
• marvel.extraction package
  • marvel.extraction.core module
    • AlleleComparator
      • AlleleComparator.compare()
    • AlleleInverter
      • AlleleInverter.add_inversed_column()
      • AlleleInverter.reorder_alleles()
    • GenotypeCounter
      • GenotypeCounter.count()
      • GenotypeCounter.count_by_category()
    • GenotypeProcessor
      • GenotypeProcessor.process_genotypes()
    • Variant
      • Variant.alt
      • Variant.chrom
      • Variant.pos
      • Variant.ref
      • Variant.rsid
      • Variant.sample_data
    • VariantProcessor
      • VariantProcessor.process()
    • count_gen()
  • marvel.extraction.extraction module
    • BgenReaderClass
      • BgenReaderClass.get_regions()
      • BgenReaderClass.read()
    • ExtractionTask
      • ExtractionTask.geno_id
      • ExtractionTask.geno_path
      • ExtractionTask.identifier
      • ExtractionTask.var_id
      • ExtractionTask.var_path
    • GeneticFileReader
      • GeneticFileReader.get_regions()
      • GeneticFileReader.read()
    • PlinkReaderClass
      • PlinkReaderClass.get_regions()
      • PlinkReaderClass.read()
    • VariantExtraction
      • VariantExtraction.execute_tasks()
      • VariantExtraction.execute_tasks_parallel()
      • VariantExtraction.setup_tasks()
    • VariantExtractor
      • VariantExtractor.extract()
    • VcfReaderClass
      • VcfReaderClass.get_regions()
      • VcfReaderClass.read()
    • extract_carriers()
  • marvel.extraction.aggregation module
    • GeneExtractor
      • GeneExtractor.extract()
    • VariantToGeneAggregator
      • VariantToGeneAggregator.aggregate()
    • extract_genes()
• marvel.utils package
  • marvel.utils.config_tools module
    • ConfigParser()
    • PipelineConfig
      • PipelineConfig.alt_column
      • PipelineConfig.association_analysis
      • PipelineConfig.cat_column
      • PipelineConfig.checkpoint_dir
      • PipelineConfig.chr_column
      • PipelineConfig.chr_pos_column
      • PipelineConfig.cov_file
      • PipelineConfig.cov_miss_error
      • PipelineConfig.covariate_models
      • PipelineConfig.exp_files
      • PipelineConfig.exposures
      • PipelineConfig.extract_variants
      • PipelineConfig.file_sep
      • PipelineConfig.force_rerun
      • PipelineConfig.from_config_dict()
      • PipelineConfig.geno_files
      • PipelineConfig.id_column
      • PipelineConfig.incl_var
      • PipelineConfig.listwise
      • PipelineConfig.max_missingness
      • PipelineConfig.min_group_size
      • PipelineConfig.n_jobs
      • PipelineConfig.neg_geno
      • PipelineConfig.outcomes
      • PipelineConfig.output_path
      • PipelineConfig.pheno_file
      • PipelineConfig.pos_column
      • PipelineConfig.prefilter_regions
      • PipelineConfig.raise_on_error
      • PipelineConfig.ref_column
      • PipelineConfig.region
      • PipelineConfig.reverse
      • PipelineConfig.stratify_models
      • PipelineConfig.stratify_overall
      • PipelineConfig.sum_geno
      • PipelineConfig.tmp_dir
      • PipelineConfig.validate()
      • PipelineConfig.var_column
      • PipelineConfig.var_files
      • PipelineConfig.var_sep
      • PipelineConfig.variant_output
    • check_config_file()
    • cnf_extract_outcome_tests()
    • cnf_extract_survival_tests()
    • create_config()
    • custom_config()
    • update_config_file()
  • marvel.utils.data_manager module
    • DataManager
      • DataManager.clear_caches()
      • DataManager.get_cache_stats()
      • DataManager.get_exposure()
      • DataManager.get_merged_data()
      • DataManager.load_covariates()
      • DataManager.load_outcome()
      • DataManager.load_outcomes()
      • DataManager.set_exposure()
    • LRUCache
      • LRUCache.clear()
      • LRUCache.get()
      • LRUCache.put()
  • marvel.utils.missingness module
    • MissingnessHandler
      • MissingnessHandler.filter_by_missingness()
      • MissingnessHandler.get_complete_columns()
      • MissingnessHandler.get_missing_summary()
      • MissingnessHandler.get_valid_ids()
      • MissingnessHandler.get_valid_ids_from_files()
      • MissingnessHandler.handle()
      • MissingnessHandler.handle_listwise()
      • MissingnessHandler.handle_pairwise()
  • marvel.utils.utils module
    • check_environ()
    • check_extension()
    • has_rows()
    • infer_column_types()
    • is_gzip()
    • load_custom()
    • merge_dfs()
    • open_file()
    • qc_dict()
    • read_if_new()
    • refactor_col()
    • return_header_list()