scout/parse/variant/frequency.py
def parse_sv_frequencies(variant):
    """Parsing of some custom sv frequencies
    
    These are very specific at the moment, this will hopefully get better over time when the
    field of structural variants is more developed.

    Args:
        variant(cyvcf2.Variant)

    Returns:
        sv_frequencies(dict)
    """
    frequency_keys = [
        'clingen_cgh_benignAF',
        'clingen_cgh_benign',
        'clingen_cgh_pathogenicAF',
        'clingen_cgh_pathogenic',
        'clingen_ngi',
        'clingen_ngiAF',
        'swegen',
        'swegenAF',
        'decipherAF',
        'decipher'
    ]
    sv_frequencies = {}

    for key in frequency_keys:
        value = variant.INFO.get(key, 0)
        if 'AF' in key:
            value = float(value)
        else:
            value = int(value)
        if value > 0:
            sv_frequencies[key] = value
    return sv_frequencies
def parse_sv_frequencies(variant):
    frequency_keys = [
        'clingen_cgh_benignAF',
        'clingen_cgh_benign',
        'clingen_cgh_pathogenicAF',
        'clingen_cgh_pathogenic',
        'clingen_ngi',
        'clingen_ngiAF',
        'swegen',
        'swegenAF',
        'decipherAF',
        'decipher'
    ]
    sv_frequencies = {}

    for key in frequency_keys:
        value = variant.INFO.get(key, 0)
        if 'AF' in key:
            value = float(value)
        else:
            value = int(value)
        if value > 0:
            sv_frequencies[key] = value
    return sv_frequencies
def parse_sv_frequencies ( variant ) : frequency_keys = [ 'clingen_cgh_benignAF' , 'clingen_cgh_benign' , 'clingen_cgh_pathogenicAF' , 'clingen_cgh_pathogenic' , 'clingen_ngi' , 'clingen_ngiAF' , 'swegen' , 'swegenAF' , 'decipherAF' , 'decipher' ] sv_frequencies = { } for key in frequency_keys : value = variant . INFO . get ( key , 0 ) if 'AF' in key : value = float ( value ) else : value = int ( value ) if value > 0 : sv_frequencies [ key ] = value return sv_frequencies
Parsing of some custom sv frequencies
    
    These are very specific at the moment, this will hopefully get better over time when the
    field of structural variants is more developed.

    Args:
        variant(cyvcf2.Variant)

    Returns:
        sv_frequencies(dict)
Parsing of some custom sv frequencies These are very specific at the moment this will hopefully get better over time when the field of structural variants is more developed .