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):
    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 ) : 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
Get the clnsig information