scout/commands/load/case.py
def case(context, vcf, vcf_sv, vcf_cancer, vcf_str, owner, ped, update, config,
         no_variants, peddy_ped, peddy_sex, peddy_check):
    """Load a case into the database.

    A case can be loaded without specifying vcf files and/or bam files
    """
    adapter = context.obj['adapter']

    if config is None and ped is None:
        LOG.warning("Please provide either scout config or ped file")
        context.abort()

    # Scout needs a config object with the neccessary information
    # If no config is used create a dictionary
    config_raw = yaml.load(config) if config else {}
    
    try:
        config_data = parse_case_data(
            config=config_raw,
            ped=ped,
            owner=owner,
            vcf_snv=vcf,
            vcf_sv=vcf_sv,
            vcf_str=vcf_str,
            vcf_cancer=vcf_cancer,
            peddy_ped=peddy_ped,
            peddy_sex=peddy_sex,
            peddy_check=peddy_check
        )
    except SyntaxError as err:
        LOG.warning(err)
        context.abort()

    LOG.info("Use family %s" % config_data['family'])
    
    try:
        case_obj = adapter.load_case(config_data, update)
    except Exception as err:
        LOG.error("Something went wrong during loading")
        LOG.warning(err)
        context.abort()
def case(context, vcf, vcf_sv, vcf_cancer, vcf_str, owner, ped, update, config,
         no_variants, peddy_ped, peddy_sex, peddy_check):
    adapter = context.obj['adapter']

    if config is None and ped is None:
        LOG.warning("Please provide either scout config or ped file")
        context.abort()

    # Scout needs a config object with the neccessary information
    # If no config is used create a dictionary
    config_raw = yaml.load(config) if config else {}
    
    try:
        config_data = parse_case_data(
            config=config_raw,
            ped=ped,
            owner=owner,
            vcf_snv=vcf,
            vcf_sv=vcf_sv,
            vcf_str=vcf_str,
            vcf_cancer=vcf_cancer,
            peddy_ped=peddy_ped,
            peddy_sex=peddy_sex,
            peddy_check=peddy_check
        )
    except SyntaxError as err:
        LOG.warning(err)
        context.abort()

    LOG.info("Use family %s" % config_data['family'])
    
    try:
        case_obj = adapter.load_case(config_data, update)
    except Exception as err:
        LOG.error("Something went wrong during loading")
        LOG.warning(err)
        context.abort()
def case ( context , vcf , vcf_sv , vcf_cancer , vcf_str , owner , ped , update , config , no_variants , peddy_ped , peddy_sex , peddy_check ) : adapter = context . obj [ 'adapter' ] if config is None and ped is None : LOG . warning ( "Please provide either scout config or ped file" ) context . abort ( ) # Scout needs a config object with the neccessary information # If no config is used create a dictionary config_raw = yaml . load ( config ) if config else { } try : config_data = parse_case_data ( config = config_raw , ped = ped , owner = owner , vcf_snv = vcf , vcf_sv = vcf_sv , vcf_str = vcf_str , vcf_cancer = vcf_cancer , peddy_ped = peddy_ped , peddy_sex = peddy_sex , peddy_check = peddy_check ) except SyntaxError as err : LOG . warning ( err ) context . abort ( ) LOG . info ( "Use family %s" % config_data [ 'family' ] ) try : case_obj = adapter . load_case ( config_data , update ) except Exception as err : LOG . error ( "Something went wrong during loading" ) LOG . warning ( err ) context . abort ( )
Load a case into the database.

    A case can be loaded without specifying vcf files and/or bam files
Load a case into the database .