trace_import_from_fofct

Reliability status: development

Convert a FOF-CT CSV file back to a pyHiM trace table in ECSV format.

Required inputs: - The path to the FOFCT file in CSV format containing the trace data. - The path to the BED file containing barcode information. - The path to a JSON file with metadata (optional).

The script will produce an ECSV file that restores the missing columns (Barcode #, Mask_id, and label).

usage: trace_import_from_fofct [-h] --fofct_file FOFCT_FILE --bed_file
                               BED_FILE [--output_file OUTPUT_FILE]

Named Arguments

--fofct_file

Path to the FOFCT file

--bed_file

Path to the BED file

--output_file

Path to the output ECSV file

Usage Example:

To convert a CSV file back to the ECSV format using the specified BED and JSON files, you would run:

trace_import_from_fofct --fofct_file output.csv --bed_file barcode.bed --output_file Trace_3D_barcode_KDtree_ROI-5.ecsv

If the --output_file argument is not provided, the script will save the ECSV file with the same name as the input CSV file but with an .ecsv extension.