malva package

Subpackages

• malva.serve package
  • Submodules
    • malva.serve.modeling module
      • setup_model()
      • parse_gene_lists()
      • handle_natural_query()
    • malva.serve.reportgen module
      • HTMLReportGenerator
    • malva.serve.serve module
      • SequenceValidationError
      • interactive_query_standard()
      • MalvaProxyFix
      • SpatialData
      • GlobalState
      • UserSession
      • create_app()
  • Module contents

Submodules

• malva.autoannotate module
  • load_marker_genes()
  • run_clustering()
  • preprocess_adata()
  • score_cells_by_cell_type()
  • get_top_cell_types()
  • annotate_clusters()
  • get_detailed_cluster_annotations()
  • analyze_technical_genes()
  • umi_threshold_cell_calling()
  • simple_good_turing_smoothing()
  • emptydrops_refinement()
  • load_markers()
  • score_annotate()
• malva.cellxmer module
  • malva_to_cellxmer()
  • malva_to_filtered_cellxmer_chunked()
• malva.cli module
  • get_index_parser()
  • setup_index_parser()
  • cmd_run_index()
  • get_show_parser()
  • setup_show_parser()
  • cmd_run_show()
  • get_quant_parser()
  • setup_quant_parser()
  • cmd_run_quant()
  • get_cellxmer_parser()
  • setup_cellxmer_parser()
  • cmd_run_cellxmer()
  • get_autoannotate_parser()
  • setup_autoannotate_parser()
  • cmd_run_autoannotate()
  • get_combine_parser()
  • setup_combine_parser()
  • cmd_run_combine()
  • get_serve_parser()
  • setup_serve_parser()
  • cmd_run_serve()
  • get_search_parser()
  • setup_search_parser()
  • cmd_run_search()
  • cmdline_args()
  • cmdline_parser()
  • cmdline_main()
• malva.combine module
  • combine_indices()
  • process_merge_chunks()
  • process_group()
  • hierarchical_combine()
• malva.complexity module
  • overlapping_windows()
  • compute_rep_vector()
  • complexity()
  • mask_low_complexity()
• malva.compressed_index module
  • LazyChunkTable
    • LazyChunkTable.__init__()
  • CompressedArrayStorage
    • CompressedArrayStorage.__init__()
    • CompressedArrayStorage.load_all_chunks_to_memory()
    • CompressedArrayStorage.unload_chunks_from_memory()
    • CompressedArrayStorage.from_array()
    • CompressedArrayStorage.from_generator()
    • CompressedArrayStorage.save()
    • CompressedArrayStorage.load()
    • CompressedArrayStorage.get_chunk()
    • CompressedArrayStorage.get_chunk_raw()
    • CompressedArrayStorage.get()
    • CompressedArrayStorage.get_batch()
    • CompressedArrayStorage.prefetch_chunks()
    • CompressedArrayStorage.get_cache_stats()
    • CompressedArrayStorage.set_cache_size()
    • CompressedArrayStorage.get_multiple_slices()
    • CompressedArrayStorage.get_slice()
    • CompressedArrayStorage.shape
    • CompressedArrayStorage.get_chunk_for_cython()
• malva.contrib module
• malva.datastore module
  • ChunkedStore
    • ChunkedStore.attrs
    • ChunkedStore.close()
    • ChunkedStore.contains()
    • ChunkedStore.copy_dataset()
    • ChunkedStore.create_dataset()
    • ChunkedStore.flush()
    • ChunkedStore.get_chunk_indices()
    • ChunkedStore.items()
    • ChunkedStore.keys()
    • ChunkedStore.resize_dataset()
    • ChunkedStore.values()
  • EliasPageCache
  • PageAlignedArray
    • PageAlignedArray.flush()
    • PageAlignedArray.get_shape()
    • PageAlignedArray.shape
  • PageCache
  • convert_h5_to_chunked()
• malva.dbutils module
  • EnsemblLocalDB
    • EnsemblLocalDB.data_dir
    • EnsemblLocalDB.index
    • EnsemblLocalDB.gene_to_ensembl
    • EnsemblLocalDB.__init__()
    • EnsemblLocalDB.database_exists()
    • EnsemblLocalDB.download_cdna_fasta()
    • EnsemblLocalDB.index_fasta()
    • EnsemblLocalDB.save_index()
    • EnsemblLocalDB.load_index()
    • EnsemblLocalDB.get_from_gene()
  • process_dna_string()
  • parse_multifasta()
  • handle_sequence()
  • process_gene_string()
  • process_ensembl_string()
  • get_from_gene()
  • get_from_ensembl()
  • validate_and_infer_query()
• malva.fast_map module
  • FastMapOfMap
    • FastMapOfMap.add()
    • FastMapOfMap.clear()
    • FastMapOfMap.extend()
    • FastMapOfMap.items()
• malva.fastq_processing module
  • FastKmerProcessor
    • FastKmerProcessor.kmer_size
    • FastKmerProcessor.overlapping
  • KmerFastqParser
    • KmerFastqParser.number_of_records
  • SequenceFastqParser
    • SequenceFastqParser.number_of_records
• malva.filter_minimizers module
  • KmerFilter
    • KmerFilter.k
    • KmerFilter.w
    • KmerFilter.num_buckets
    • KmerFilter.filter_stream()
    • KmerFilter.k
    • KmerFilter.num_buckets
    • KmerFilter.w
  • filter_kmers()
• malva.index module
  • load_flavor()
• malva.indexes module
  • BackgroundModel
    • BackgroundModel.total_mers
    • BackgroundModel.kmer_size
    • BackgroundModel.verbose
    • BackgroundModel.create_from_reference()
    • BackgroundModel.export_fasta()
    • BackgroundModel.import_jellyfish_fasta()
    • BackgroundModel.is_mer_above_cutoff()
    • BackgroundModel.load()
    • BackgroundModel.save()
  • MalvaIndex
    • MalvaIndex.index_dir
    • MalvaIndex.kmer_size
    • MalvaIndex.verbose
    • MalvaIndex.n_chunks
    • MalvaIndex.add_reads()
    • MalvaIndex.close()
    • MalvaIndex.coord_lims
    • MalvaIndex.data_lengths
    • MalvaIndex.get_cell_id()
    • MalvaIndex.get_project_id()
    • MalvaIndex.get_whole_sliding_sequence()
    • MalvaIndex.get_whole_sliding_sequence_chunk()
    • MalvaIndex.index
    • MalvaIndex.index_dir
    • MalvaIndex.index_exists()
    • MalvaIndex.index_file
    • MalvaIndex.initialize()
    • MalvaIndex.initialize_kmer_index()
    • MalvaIndex.jump_amount
    • MalvaIndex.kmer_size
    • MalvaIndex.load_index_to_memory()
    • MalvaIndex.merge_chunks()
    • MalvaIndex.n_chunks
    • MalvaIndex.n_spatial
    • MalvaIndex.open()
    • MalvaIndex.project_mapping
    • MalvaIndex.set_background_model()
    • MalvaIndex.set_barcode_index()
    • MalvaIndex.set_spatial_coords()
    • MalvaIndex.set_spatial_index()
    • MalvaIndex.spatial_coord
    • MalvaIndex.verbose
    • MalvaIndex.where()
    • MalvaIndex.write()
  • SpatialIndex
    • SpatialIndex.get_coords()
    • SpatialIndex.get_coords_stomics()
    • SpatialIndex.load_binary()
    • SpatialIndex.load_binary_stomics()
    • SpatialIndex.num_items()
    • SpatialIndex.save_binary()
  • create_singlecell_index()
  • create_spatial_index()
• malva.kmer_processing module
  • FastKmerExtractor
  • decode_kmer()
  • encode_kmer()
  • get_kmers_numeric()
  • get_sliding_kmers_numeric()
• malva.quant module
  • MalvaReferenceNotFound
  • write_mtx_header()
  • process_batch()
  • resave_h5ad()
  • process_reference()
• malva.reader module
  • iterate_fasta()
  • iterate_flavor()
• malva.search module
  • read_sequences_file()
  • check_server_connection()
  • submit_search_job()
  • get_datasets()
  • get_job_status()
  • format_results()
  • wait_for_completion()
• malva.show module
  • MalvaPlot
    • MalvaPlot.__init__()
    • MalvaPlot.scatter()
    • MalvaPlot.image()
• malva.spacemake module
  • nonsingular()
  • create_mesh()
  • binning_hexagon()
  • aggregate_adata_by_indices()
  • create_meshed_adata()
• malva.utils module
  • FormatError
    • FormatError.__init__()
  • check_cell_string()
  • conditional_track()
  • safety_check_eval()
  • get_module_path()
  • save_pickle()
  • load_pickle()
  • check_file_exists()
  • check_directory_exists()
  • check_adata_structure()
  • load_properties_from_adata()
  • check_obs_unique()
  • copytree2()
  • get_package_path()
  • get_absolute_package_path()
  • h5_to_dict()
  • write_key_to_h5()
  • binary_search()
  • group_intervals()
  • defragment_hdf5_file()
  • download_url_to_file()
  • get_reference_cache()
  • convert_to_bytes()
• malva.xopen module
  • xopen()

Module contents