cellprofile

Function

cellprofile(
    self,
    tool_cna_files: List[str],
    tool_names: List[str],
    outfile: str = "unique_cell_profile.csv"
) -> None

This function counts the number of unique cells contained in each tool’s CNA result file and exports a summary table to self.output_dir.

Parameters

Name	Type	Description
tool_cna_files	List[str]	List of CNA result file paths produced by different tools. Must be aligned with tool_names by order.
tool_names	List[str]	List of tool names. Used as the row index in the output table. Must have the same length as tool_cna_files.
outfile	str	The name of the output CSV file. Defaults to "unique_cell_profile.csv".

Output

The function writes a single CSV file:

• Path: os.path.join(self.output_dir, outfile)
• Columns:
• unique_cells_profile: the number of unique cells for each tool
• Index:
• Tool: tool name (from tool_names)

Example output (unique_cell_profile.csv):

Tool,unique_cells_profile
CHISEL,1099
Alleloscope,1050
SIGNALS,980

Example

rom hcbench.gtbench import gtbench

runner = gtbench.GTBench(output_dir="out/gt_output/")

tool_cna_files = [
    "out/chisel/haplotype_combined.csv",
    "out/signals/haplotype_combined.csv",
    "out/alleloscope/haplotype_combined.csv",
]
tool_names = ["CHISEL", "SIGNALS", "Alleloscope"]

runner.cellprofile(
    tool_cna_files=tool_cna_files,
    tool_names=tool_names,
    outfile="unique_cell_profile.csv"
)