INNER CODE UNIT · Python

read_bed

hillerlab/TOGA · CESAR_wrapper.py:310

def read_bed(gene, bed_file):
    """Extract and parse gene-related bed track."""
    try:  # if it's berkeley db file
        bed_track_raw = bed_extract_id(bed_file, gene)
    except OSError:
        # h5df cannot open this file: this is likely a text file
        bed_track_raw = bed_extract_id_text(bed_file, gene)

    # left CDS only
    bed_track = make_cds_track(bed_track_raw)

    # regular parsing of a bed-12 formatted file
    bed_info = bed_track.split("\t")

    # if not 12 fields -> then input is wrong
    die("Error! Bed-12 required!", 1) if len(bed_info) != 12 else None
    bed_data = {
        "chrom": bed_info[0],

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