scout/parse/variant/clnsig.py
def parse_clnsig(acc, sig, revstat, transcripts):
    """Get the clnsig information

    Args:
        acc(str): The clnsig accession number, raw from vcf
        sig(str): The clnsig significance score, raw from vcf
        revstat(str): The clnsig revstat, raw from vcf
        transcripts(iterable(dict))

    Returns:
        clnsig_accsessions(list): A list with clnsig accessions
    """
    clnsig_accsessions = []

    if acc:
    # New format of clinvar allways have integers as accession numbers
        try:
            acc = int(acc)
        except ValueError:
            pass
        # There are sometimes different separators so we need to check which
        # one to use
        if isinstance(acc, int):
            revstat_groups = []
            if revstat:
                revstat_groups = [rev.lstrip('_') for rev in revstat.split(',')]

            sig_groups = []
            if sig:
                for significance in sig.split('/'):
                    splitted_word = significance.split('_')
                    sig_groups.append(' '.join(splitted_word[:2]))

            for sign_term in sig_groups:
                clnsig_accsessions.append({
                    'value': sign_term,
                    'accession': int(acc),
                    'revstat': ', '.join(revstat_groups),
                })
        else:
            # There are sometimes different separators so we need to check which
            # one to use
            acc_groups = acc.split('|')
            sig_groups = sig.split('|')
            revstat_groups = revstat.split('|')
            for acc_group, sig_group, revstat_group in zip(acc_groups, sig_groups, revstat_groups):
                accessions = acc_group.split(',')
                significances = sig_group.split(',')
                revstats = revstat_group.split(',')
                for accession, significance, revstat in zip(accessions, significances, revstats):
                    clnsig_accsessions.append({
                        'value': int(significance),
                        'accession': accession,
                        'revstat': revstat,
                    })

    elif transcripts:
        clnsig = set()
        for transcript in transcripts:
            for annotation in transcript.get('clinsig', []):
                clnsig.add(annotation)
        for annotation in clnsig:
            clnsig_accsessions.append({'value': annotation})

    return clnsig_accsessions
def parse_clnsig(acc, sig, revstat, transcripts):
    """Get the clnsig information

    Args:
        acc(str): The clnsig accession number, raw from vcf
        sig(str): The clnsig significance score, raw from vcf
        revstat(str): The clnsig revstat, raw from vcf
        transcripts(iterable(dict))

    Returns:
        clnsig_accsessions(list): A list with clnsig accessions
    """
    clnsig_accsessions = []

    if acc:
    # New format of clinvar allways have integers as accession numbers
        try:
            acc = int(acc)
        except ValueError:
            pass
        # There are sometimes different separators so we need to check which
        # one to use
        if isinstance(acc, int):
            revstat_groups = []
            if revstat:
                revstat_groups = [rev.lstrip('_') for rev in revstat.split(',')]

            sig_groups = []
            if sig:
                for significance in sig.split('/'):
                    splitted_word = significance.split('_')
                    sig_groups.append(' '.join(splitted_word[:2]))

            for sign_term in sig_groups:
                clnsig_accsessions.append({
                    'value': sign_term,
                    'accession': int(acc),
                    'revstat': ', '.join(revstat_groups),
                })
        else:
            # There are sometimes different separators so we need to check which
            # one to use
            acc_groups = acc.split('|')
            sig_groups = sig.split('|')
            revstat_groups = revstat.split('|')
            for acc_group, sig_group, revstat_group in zip(acc_groups, sig_groups, revstat_groups):
                accessions = acc_group.split(',')
                significances = sig_group.split(',')
                revstats = revstat_group.split(',')
                for accession, significance, revstat in zip(accessions, significances, revstats):
                    clnsig_accsessions.append({
                        'value': int(significance),
                        'accession': accession,
                        'revstat': revstat,
                    })

    elif transcripts:
        clnsig = set()
        for transcript in transcripts:
            for annotation in transcript.get('clinsig', []):
                clnsig.add(annotation)
        for annotation in clnsig:
            clnsig_accsessions.append({'value': annotation})

    return clnsig_accsessions
Get the clnsig information

    Args:
        acc(str): The clnsig accession number, raw from vcf
        sig(str): The clnsig significance score, raw from vcf
        revstat(str): The clnsig revstat, raw from vcf
        transcripts(iterable(dict))

    Returns:
        clnsig_accsessions(list): A list with clnsig accessions