INNER CODE UNIT · Python

olap_gtf

BirolLab/straglr · straglr_compare.py:209

def olap_gtf(bed, gtf_file):
    gtf = BedTool(gtf_file)

    skipped_types = ('retained_intron', 'nonsense_mediated_decay', 'processed_transcript')
    olaps = defaultdict(list)
    assigned = {}
    for cols in bed.intersect(gtf, wao=True, f=1.0):
        locus = tuple(cols[:3])

        if cols[3] == '.':
            assigned[locus] = None
            continue
        feature = cols[5]

        gff = create_interval_from_list(cols[3:-1])
        gene = gff.attrs['gene_name']
        transcript = None
        transcript_type = None

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