INNER CODE UNIT · Python

parse_gff

cbg-ethz/V-pipe · workflow/scripts/assemble_visualization_webpage.py:80

def parse_gff(fname):
    """Convert GFF to map."""
    features = []

    print(f'Parsing GFF: "{fname}"')
    with open(fname) as fd:
        for record in GFF.parse(fd):
            for feature in record.features:
                features.append(
                    {
                        "id": record.id,
                        "type": feature.type,
                        "name": feature.qualifiers.get("Name", [feature.id])[0],
                        "start": int(feature.location.start),
                        "end": int(feature.location.end),
                    }
                )
    return features

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