API Reference

This section documents the Malva Python API and the full algorithmic framework underlying index construction and querying. The algorithmic documentation is intended to enable re-implementation and reproducibility; the Python API exposes the components available via the open-source distribution.

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Algorithmic Framework

The indexing and query algorithms are fully documented below, including data structures, pseudocode, and default parameters.

• Indexing & Query Framework
  • Definitions
  • Data Structure
• Index Construction
  • K-mer Encoding and Sampling
• Querying
  • Window-Based Matching
  • Query Batching and Index Access Pattern
• Parameters Summary

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Python Modules

The following modules are available in the open-source Python distribution:

• 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.fastq_processing module
  • FastKmerProcessor
    • FastKmerProcessor.kmer_size
    • FastKmerProcessor.overlapping
  • KmerFastqParser
    • KmerFastqParser.number_of_records
  • SequenceFastqParser
    • SequenceFastqParser.number_of_records
• 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.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()