netmap.masking.external.preprocess_bed_file

netmap.masking.external.preprocess_bed_file(bed_file)

Read a BED file and parse the TF motif list column.

Loads a tab-separated BED file describing cis-regulatory modules (CRMs) and splits the comma-separated TF list into a Python list for downstream use by get_regulators().

Parameters:

bed_file (str) – Path to the BED file. Expected columns (0-indexed) are chr, start, end, TF_list, TF_number, strand, number1, number2, large_number.

Returns:

DataFrame with the original BED columns plus an additional TF_list_list column containing each TF name as a Python list element.

Return type:

pd.DataFrame