pLAST documentation

MODULES - API

• alignment module
  • Alignment
  • is_unknown()
  • rotate()
  • count_inversions()
  • extract_module_pairs()
  • mapping_and_crossings()
  • best_layout_min_crossings()
  • rotate_parsed()
  • rotate_plasmid()
• data module
  • PLASTData
    • PLASTData.get_metadata_index_name()
    • PLASTData.resolve_accession()
    • PLASTData.accession_in_metadata_index()
    • PLASTData.filter_ids_for_metadata_index()
    • PLASTData.candidate_accessions()
    • PLASTData.get_metadata_row()
    • PLASTData.get_metadata_for_ids()
    • PLASTData.get_search_index()
    • PLASTData.get_model_ids_and_umap_coords()
    • PLASTData.warm_search_indexes()
    • PLASTData.get_cluster_mapping()
    • PLASTData.get_cluster_lookup()
    • PLASTData.get_mmseqs_db()
    • PLASTData.get_model()
• exceptions module
  • DataLoadingError
  • NotFoundError
  • BadToken
• model module
  • PLASTModel
    • PLASTModel.model
    • PLASTModel.embeddings
    • PLASTModel.mean_embedding
    • PLASTModel.idf
    • PLASTModel.umap_mapper
• parsers module
  • read_fasta()
  • read_m8()
  • read_gbff()
  • read_emapper_hits()
  • read_hmmscan_output()
• plast module
  • PLAST
    • PLAST.copy()
    • PLAST.to_dict()
    • PLAST.from_dict()
    • PLAST.to_json()
    • PLAST.from_json()
    • PLAST.log()
    • PLAST.error()
    • PLAST.debug()
    • PLAST.tmp_dir()
    • PLAST.get_by_accession()
    • PLAST.load_gbff()
    • PLAST.load_nt_fasta()
    • PLAST.assign_mmseqs_clusters()
    • PLAST.assign_eggnog_annot()
    • PLAST.encode()
    • PLAST.get_most_similar()
    • PLAST.module_search()
    • PLAST.draw_network()
• utils module
  • is_gpu_available()
  • euclidean()
  • cosine_similarity_numba()
  • warm_page_cache()

TUTORIALS

• Notebooks
  • Installation
  • Basic pLAST usage

LINKS

• GitHub
• pLAST-interface
• figshare
• LBS