gunz_cm.cli package

Submodules

gunz_cm.cli.converters.hic2cool(input: str = <typer.models.ArgumentInfo object>, output: str = <typer.models.ArgumentInfo object>, resolution: int = <typer.models.OptionInfo object>, nproc: int = <typer.models.OptionInfo object>, dry_run: bool = <typer.models.OptionInfo object>)[source]: Converts .hic to .cool format.

gunz_cm.cli.converters.to_bigmat(resolution: int = <typer.models.ArgumentInfo object>, region1: str = <typer.models.ArgumentInfo object>, input: str = <typer.models.ArgumentInfo object>, output: str = <typer.models.ArgumentInfo object>, region2: str | None = <typer.models.OptionInfo object>, balancing: str = <typer.models.OptionInfo object>, no_full_matrix: bool = <typer.models.OptionInfo object>, verify_result: bool = <typer.models.OptionInfo object>, dry_run: bool = <typer.models.OptionInfo object>)[source]: Converts contact matrix data to a bigmat (memmap) format.

gunz_cm.cli.converters.to_coo(region1: str = <typer.models.ArgumentInfo object>, resolution: int = <typer.models.ArgumentInfo object>, balancing: str = <typer.models.ArgumentInfo object>, input: str = <typer.models.ArgumentInfo object>, output: str = <typer.models.ArgumentInfo object>, region2: str | None = <typer.models.OptionInfo object>, res_to_one: bool = <typer.models.OptionInfo object>, output_delimiter: str = <typer.models.OptionInfo object>, to_mcoo: bool = <typer.models.OptionInfo object>, gen_pseudo_weights: bool = <typer.models.OptionInfo object>, dry_run: bool = <typer.models.OptionInfo object>)[source]: Converts contact matrix data to a COO format.

gunz_cm.cli.converters.to_intra_cm_coos(resolution: int = <typer.models.ArgumentInfo object>, balancing: str = <typer.models.ArgumentInfo object>, input: str = <typer.models.ArgumentInfo object>, output: str = <typer.models.ArgumentInfo object>, region2: str | None = <typer.models.OptionInfo object>, res_to_one: bool = <typer.models.OptionInfo object>, output_delimiter: str = <typer.models.OptionInfo object>, to_mcoo: bool = <typer.models.OptionInfo object>, gen_pseudo_weights: bool = <typer.models.OptionInfo object>, dry_run: bool = <typer.models.OptionInfo object>)[source]: Converts all intra-chromosomal contact matrices to COO format.

gunz_cm.cli.loaders.get_balancing(input_path: str = <typer.models.ArgumentInfo object>, resolution: int = <typer.models.ArgumentInfo object>, chrom: str = <typer.models.ArgumentInfo object>)[source]: Gets available balancing methods for a region in a .hic or .cool file.

gunz_cm.cli.loaders.get_bins(input_path: str = <typer.models.ArgumentInfo object>, resolution: int = <typer.models.ArgumentInfo object>)[source]: Gets the binnified index from a .hic or .cool file.

gunz_cm.cli.loaders.get_chrom_infos(input_path: str = <typer.models.ArgumentInfo object>)[source]: Queries chromosome names and lengths from a .hic or .cool file.

gunz_cm.cli.loaders.get_resolutions(input_path: str = <typer.models.ArgumentInfo object>)[source]: Gets the resolutions available in a contact matrix file.

gunz_cm.cli.loaders.load_data(input_path: str = <typer.models.ArgumentInfo object>, resolution: int = <typer.models.ArgumentInfo object>, region1: str | None = <typer.models.OptionInfo object>, region2: str | None = <typer.models.OptionInfo object>, balancing: str | None = <typer.models.OptionInfo object>, output_format: DataStructure = <typer.models.OptionInfo object>)[source]: Loads contact matrix data and displays a summary.

gunz_cm.cli.main.main(verbose: bool = <typer.models.OptionInfo object>)[source]: CM Library Main CLI