d23794e515aac062b94c9e492143d97ec55c9cc9,src/pyscenic/cli/pyscenic.py,,aucell_command,#Any#,172

Before Change

    LOGGER.info("Loading expression matrix.")
    ex_mtx = _load_expression_matrix(args)

    if any(args.regulons_fname.name.endswith(ext) for ext in FILE_EXTENSION2SEPARATOR.keys()):
        LOGGER.info("Creating regulons.")
        regulons = _df2regulons(args.regulons_fname.name)
    elif args.regulons_fname.name.endswith(".gmt"):
        LOGGER.info("Loading regulons.")
        regulons = GeneSignature.from_gmt(args.regulons_fname.name,
                                           field_separator="\t", gene_separator="\t")
    else:
        LOGGER.info("Loading regulons.")
        regulons = _load_modules(args.regulons_fname.name)

    LOGGER.info("Calculating enrichment.")
    auc_heatmap = aucell(ex_mtx, regulons, auc_threshold=args.auc_threshold,
                         noweights=args.weights != "yes", num_workers=args.num_workers)

After Change

    Calculate regulon enrichment (as AUC values) for cells.
    
    LOGGER.info("Loading expression matrix.")
    try:
        ex_mtx = load_exp_matrix(args.expression_mtx_fname.name, (args.transpose == "yes"))
    except ValueError as e:
        LOGGER.error(e)
        sys.exit(1)

    LOGGER.info("Loading gene signatures.")
    try:
        signatures = load_signatures(args.signatures_fname.name)
    except ValueError as e:

Instances