Source code for

from pathlib import Path
from typing import Union

import pandas as pd

from pandas_genomics.scalars import Region

[docs]def from_bed(filename: Union[str, Path]): """ Yields genomic regions from a bed file as Region scalars Parameters ---------- filename: str or Path bed file Returns ------- List[Region] """ with open(filename, "r") as input: for idx, line in enumerate(input): if ( line.startswith("browser") or line.startswith("track") or line.startswith("#") ): continue line = line.split("\t") if len(line) < 3: raise ValueError( f"Expected at least 3 tab-delimited fields, found {len(line)} in '{line}'." ) # Note that positions need to be incremented by 1 to go from 0-based to 1-based. yield Region(line[0], int(line[1]) + 1, int(line[2]) + 1, line[3])