vcf2clinvar/clinvar.py
def _parse_frequencies(self):
        """Parse frequency data in ClinVar VCF"""
        frequencies = OrderedDict([
            ('EXAC', 'Unknown'),
            ('ESP', 'Unknown'),
            ('TGP', 'Unknown')])
        pref_freq = 'Unknown'
        for source in frequencies.keys():
            freq_key = 'AF_' + source
            if freq_key in self.info:
                frequencies[source] = self.info[freq_key]
                if pref_freq == 'Unknown':
                    pref_freq = frequencies[source]
        return pref_freq, frequencies
def _parse_frequencies(self):
        """Parse frequency data in ClinVar VCF"""
        frequencies = OrderedDict([
            ('EXAC', 'Unknown'),
            ('ESP', 'Unknown'),
            ('TGP', 'Unknown')])
        pref_freq = 'Unknown'
        for source in frequencies.keys():
            freq_key = 'AF_' + source
            if freq_key in self.info:
                frequencies[source] = self.info[freq_key]
                if pref_freq == 'Unknown':
                    pref_freq = frequencies[source]
        return pref_freq, frequencies
def _parse_frequencies ( self ) : frequencies = OrderedDict ( [ ( 'EXAC' , 'Unknown' ) , ( 'ESP' , 'Unknown' ) , ( 'TGP' , 'Unknown' ) ] ) pref_freq = 'Unknown' for source in frequencies . keys ( ) : freq_key = 'AF_' + source if freq_key in self . info : frequencies [ source ] = self . info [ freq_key ] if pref_freq == 'Unknown' : pref_freq = frequencies [ source ] return pref_freq , frequencies
Parse frequency data in ClinVar VCF
Parse frequency data in ClinVar VCF