scout/load/all.py
def load_region(adapter, case_id, hgnc_id=None, chrom=None, start=None, end=None):
    """Load all variants in a region defined by a HGNC id

    Args:
        adapter (MongoAdapter)
        case_id (str): Case id
        hgnc_id (int): If all variants from a gene should be uploaded
        chrom (str): If variants from coordinates should be uploaded
        start (int): Start position for region
        end (int): Stop position for region
    """
    if hgnc_id:
        gene_obj = adapter.hgnc_gene(hgnc_id)
        if not gene_obj:
            ValueError("Gene {} does not exist in database".format(hgnc_id))
        chrom = gene_obj['chromosome']
        start = gene_obj['start']
        end = gene_obj['end']

    case_obj = adapter.case(case_id=case_id)
    if not case_obj:
        raise ValueError("Case {} does not exist in database".format(case_id))

    log.info("Load clinical SNV variants for case: {0} region: chr {1}, start"
             " {2}, end {3}".format(case_obj['_id'], chrom, start, end))

    adapter.load_variants(case_obj=case_obj, variant_type='clinical',
                          category='snv', chrom=chrom, start=start, end=end)

    vcf_sv_file = case_obj['vcf_files'].get('vcf_sv')
    if vcf_sv_file:
        log.info("Load clinical SV variants for case: {0} region: chr {1}, "
                 "start {2}, end {3}".format(case_obj['_id'], chrom, start, end))
        adapter.load_variants(case_obj=case_obj, variant_type='clinical',
                              category='sv', chrom=chrom, start=start, end=end)

    vcf_str_file = case_obj['vcf_files'].get('vcf_str')
    if vcf_str_file: 
        log.info("Load clinical STR variants for case: {0} region: chr {1}, "
                 "start {2}, end {3}".format(case_obj['_id'], chrom, start, end))
        adapter.load_variants(case_obj=case_obj, variant_type='clinical',
                              category='str', chrom=chrom, start=start, end=end)

    if case_obj['is_research']:
        log.info("Load research SNV variants for case: {0} region: chr {1}, "
                 "start {2}, end {3}".format(case_obj['_id'], chrom, start, end))
        adapter.load_variants(case_obj=case_obj, variant_type='research',
                              category='snv', chrom=chrom, start=start, end=end)

        vcf_sv_research = case_obj['vcf_files'].get('vcf_sv_research')
        if vcf_sv_research:
            log.info("Load research SV variants for case: {0} region: chr {1},"
                     " start {2}, end {3}".format(case_obj['_id'], chrom, start, end))
            adapter.load_variants(case_obj=case_obj, variant_type='research',
                                  category='sv', chrom=chrom, start=start, end=end)
def load_region(adapter, case_id, hgnc_id=None, chrom=None, start=None, end=None):
    """Load all variants in a region defined by a HGNC id

    Args:
        adapter (MongoAdapter)
        case_id (str): Case id
        hgnc_id (int): If all variants from a gene should be uploaded
        chrom (str): If variants from coordinates should be uploaded
        start (int): Start position for region
        end (int): Stop position for region
    """
    if hgnc_id:
        gene_obj = adapter.hgnc_gene(hgnc_id)
        if not gene_obj:
            ValueError("Gene {} does not exist in database".format(hgnc_id))
        chrom = gene_obj['chromosome']
        start = gene_obj['start']
        end = gene_obj['end']

    case_obj = adapter.case(case_id=case_id)
    if not case_obj:
        raise ValueError("Case {} does not exist in database".format(case_id))

    log.info("Load clinical SNV variants for case: {0} region: chr {1}, start"
             " {2}, end {3}".format(case_obj['_id'], chrom, start, end))

    adapter.load_variants(case_obj=case_obj, variant_type='clinical',
                          category='snv', chrom=chrom, start=start, end=end)

    vcf_sv_file = case_obj['vcf_files'].get('vcf_sv')
    if vcf_sv_file:
        log.info("Load clinical SV variants for case: {0} region: chr {1}, "
                 "start {2}, end {3}".format(case_obj['_id'], chrom, start, end))
        adapter.load_variants(case_obj=case_obj, variant_type='clinical',
                              category='sv', chrom=chrom, start=start, end=end)

    vcf_str_file = case_obj['vcf_files'].get('vcf_str')
    if vcf_str_file: 
        log.info("Load clinical STR variants for case: {0} region: chr {1}, "
                 "start {2}, end {3}".format(case_obj['_id'], chrom, start, end))
        adapter.load_variants(case_obj=case_obj, variant_type='clinical',
                              category='str', chrom=chrom, start=start, end=end)

    if case_obj['is_research']:
        log.info("Load research SNV variants for case: {0} region: chr {1}, "
                 "start {2}, end {3}".format(case_obj['_id'], chrom, start, end))
        adapter.load_variants(case_obj=case_obj, variant_type='research',
                              category='snv', chrom=chrom, start=start, end=end)

        vcf_sv_research = case_obj['vcf_files'].get('vcf_sv_research')
        if vcf_sv_research:
            log.info("Load research SV variants for case: {0} region: chr {1},"
                     " start {2}, end {3}".format(case_obj['_id'], chrom, start, end))
            adapter.load_variants(case_obj=case_obj, variant_type='research',
                                  category='sv', chrom=chrom, start=start, end=end)
def load_region ( adapter , case_id , hgnc_id = None , chrom = None , start = None , end = None ) : if hgnc_id : gene_obj = adapter . hgnc_gene ( hgnc_id ) if not gene_obj : ValueError ( "Gene {} does not exist in database" . format ( hgnc_id ) ) chrom = gene_obj [ 'chromosome' ] start = gene_obj [ 'start' ] end = gene_obj [ 'end' ] case_obj = adapter . case ( case_id = case_id ) if not case_obj : raise ValueError ( "Case {} does not exist in database" . format ( case_id ) ) log . info ( "Load clinical SNV variants for case: {0} region: chr {1}, start" " {2}, end {3}" . format ( case_obj [ '_id' ] , chrom , start , end ) ) adapter . load_variants ( case_obj = case_obj , variant_type = 'clinical' , category = 'snv' , chrom = chrom , start = start , end = end ) vcf_sv_file = case_obj [ 'vcf_files' ] . get ( 'vcf_sv' ) if vcf_sv_file : log . info ( "Load clinical SV variants for case: {0} region: chr {1}, " "start {2}, end {3}" . format ( case_obj [ '_id' ] , chrom , start , end ) ) adapter . load_variants ( case_obj = case_obj , variant_type = 'clinical' , category = 'sv' , chrom = chrom , start = start , end = end ) vcf_str_file = case_obj [ 'vcf_files' ] . get ( 'vcf_str' ) if vcf_str_file : log . info ( "Load clinical STR variants for case: {0} region: chr {1}, " "start {2}, end {3}" . format ( case_obj [ '_id' ] , chrom , start , end ) ) adapter . load_variants ( case_obj = case_obj , variant_type = 'clinical' , category = 'str' , chrom = chrom , start = start , end = end ) if case_obj [ 'is_research' ] : log . info ( "Load research SNV variants for case: {0} region: chr {1}, " "start {2}, end {3}" . format ( case_obj [ '_id' ] , chrom , start , end ) ) adapter . load_variants ( case_obj = case_obj , variant_type = 'research' , category = 'snv' , chrom = chrom , start = start , end = end ) vcf_sv_research = case_obj [ 'vcf_files' ] . get ( 'vcf_sv_research' ) if vcf_sv_research : log . info ( "Load research SV variants for case: {0} region: chr {1}," " start {2}, end {3}" . format ( case_obj [ '_id' ] , chrom , start , end ) ) adapter . load_variants ( case_obj = case_obj , variant_type = 'research' , category = 'sv' , chrom = chrom , start = start , end = end )
Load all variants in a region defined by a HGNC id

    Args:
        adapter (MongoAdapter)
        case_id (str): Case id
        hgnc_id (int): If all variants from a gene should be uploaded
        chrom (str): If variants from coordinates should be uploaded
        start (int): Start position for region
        end (int): Stop position for region
Load all variants in a region defined by a HGNC id