bed_distance_wrapper#

RNAdist.fasta_wrappers.bed_distance_wrapper(fasta: str, beds: List[str], md_config: Dict[str, Any], names: List[str] = None, num_threads: int = 1)#

Command Line Wrapper for binding site distance calculation.

This will use fasta files and bed files of binding sites to calculate expected distances of pairwise binding sites. The output will be stored in a TSV file specified via outfile.

Parameters:

  • fasta (str) – Path to a fasta file

  • beds (List[str]) – List of multiple bed file paths. The bed files must contain first columns matching entries from the fasta headers

  • md_config (Dict[str, Any]) – A dictionary containing keys and values to set up the ViennaRNA Model details

  • names – The names for bed files displayed in the output file if not provided (default) it will use the filenames

  • num_threads (int) – number of parallel processes to use

Returns: pd.Dataframe

pandas dataframe with the following columns:

“seq_name”, “name1”, “start1”, “stop1”, “name2”, “start2”, “stop2”, “expected_distance”

seq_name is the header within the fasta sequence or the first column in the bed files name is the name for the bed file specified via names start and stop correspong to the binding sites