scout/server/blueprints/variants/controllers.py
def clinsig_human(variant_obj):
    """Convert to human readable version of CLINSIG evaluation."""
    for clinsig_obj in variant_obj['clnsig']:
        # The clinsig objects allways have a accession
        if isinstance(clinsig_obj['accession'], int):
            # New version
            link = "https://www.ncbi.nlm.nih.gov/clinvar/variation/{}"
        else:
            # Old version
            link = "https://www.ncbi.nlm.nih.gov/clinvar/{}"

        human_str = 'not provided'
        if clinsig_obj.get('value'):
            try:
                # Old version
                int(clinsig_obj['value'])
                human_str = CLINSIG_MAP.get(clinsig_obj['value'], 'not provided')
            except ValueError:
                # New version
                human_str = clinsig_obj['value']

        clinsig_obj['human'] = human_str
        clinsig_obj['link'] = link.format(clinsig_obj['accession'])

        yield clinsig_obj
def clinsig_human(variant_obj):
    for clinsig_obj in variant_obj['clnsig']:
        # The clinsig objects allways have a accession
        if isinstance(clinsig_obj['accession'], int):
            # New version
            link = "https://www.ncbi.nlm.nih.gov/clinvar/variation/{}"
        else:
            # Old version
            link = "https://www.ncbi.nlm.nih.gov/clinvar/{}"

        human_str = 'not provided'
        if clinsig_obj.get('value'):
            try:
                # Old version
                int(clinsig_obj['value'])
                human_str = CLINSIG_MAP.get(clinsig_obj['value'], 'not provided')
            except ValueError:
                # New version
                human_str = clinsig_obj['value']

        clinsig_obj['human'] = human_str
        clinsig_obj['link'] = link.format(clinsig_obj['accession'])

        yield clinsig_obj
def clinsig_human ( variant_obj ) : for clinsig_obj in variant_obj [ 'clnsig' ] : # The clinsig objects allways have a accession if isinstance ( clinsig_obj [ 'accession' ] , int ) : # New version link = "https://www.ncbi.nlm.nih.gov/clinvar/variation/{}" else : # Old version link = "https://www.ncbi.nlm.nih.gov/clinvar/{}" human_str = 'not provided' if clinsig_obj . get ( 'value' ) : try : # Old version int ( clinsig_obj [ 'value' ] ) human_str = CLINSIG_MAP . get ( clinsig_obj [ 'value' ] , 'not provided' ) except ValueError : # New version human_str = clinsig_obj [ 'value' ] clinsig_obj [ 'human' ] = human_str clinsig_obj [ 'link' ] = link . format ( clinsig_obj [ 'accession' ] ) yield clinsig_obj
Convert to human readable version of CLINSIG evaluation.
Convert to human readable version of CLINSIG evaluation .