scout/commands/export/variant.py
def variants(context, collaborator, document_id, case_id, json):
    """Export causatives for a collaborator in .vcf format"""
    LOG.info("Running scout export variants")
    adapter = context.obj['adapter']
    collaborator = collaborator or 'cust000'

    variants = export_variants(
        adapter,
        collaborator,
        document_id=document_id,
        case_id=case_id
    )

    if json:
        click.echo(dumps([var for var in variants]))
        return

    vcf_header = VCF_HEADER

    #If case_id is given, print more complete vcf entries, with INFO,
    #and genotypes
    if case_id:
        vcf_header[-1] = vcf_header[-1] + "\tFORMAT"
        case_obj = adapter.case(case_id=case_id)
        for individual in case_obj['individuals']:
            vcf_header[-1] = vcf_header[-1] + "\t" + individual['individual_id']

    #print header
    for line in vcf_header:
        click.echo(line)

    for variant_obj in variants:
        variant_string = get_vcf_entry(variant_obj, case_id=case_id)
        click.echo(variant_string)
def variants(context, collaborator, document_id, case_id, json):
    LOG.info("Running scout export variants")
    adapter = context.obj['adapter']
    collaborator = collaborator or 'cust000'

    variants = export_variants(
        adapter,
        collaborator,
        document_id=document_id,
        case_id=case_id
    )

    if json:
        click.echo(dumps([var for var in variants]))
        return

    vcf_header = VCF_HEADER

    #If case_id is given, print more complete vcf entries, with INFO,
    #and genotypes
    if case_id:
        vcf_header[-1] = vcf_header[-1] + "\tFORMAT"
        case_obj = adapter.case(case_id=case_id)
        for individual in case_obj['individuals']:
            vcf_header[-1] = vcf_header[-1] + "\t" + individual['individual_id']

    #print header
    for line in vcf_header:
        click.echo(line)

    for variant_obj in variants:
        variant_string = get_vcf_entry(variant_obj, case_id=case_id)
        click.echo(variant_string)
def variants ( context , collaborator , document_id , case_id , json ) : LOG . info ( "Running scout export variants" ) adapter = context . obj [ 'adapter' ] collaborator = collaborator or 'cust000' variants = export_variants ( adapter , collaborator , document_id = document_id , case_id = case_id ) if json : click . echo ( dumps ( [ var for var in variants ] ) ) return vcf_header = VCF_HEADER #If case_id is given, print more complete vcf entries, with INFO, #and genotypes if case_id : vcf_header [ - 1 ] = vcf_header [ - 1 ] + "\tFORMAT" case_obj = adapter . case ( case_id = case_id ) for individual in case_obj [ 'individuals' ] : vcf_header [ - 1 ] = vcf_header [ - 1 ] + "\t" + individual [ 'individual_id' ] #print header for line in vcf_header : click . echo ( line ) for variant_obj in variants : variant_string = get_vcf_entry ( variant_obj , case_id = case_id ) click . echo ( variant_string )
Export causatives for a collaborator in .vcf format
Export causatives for a collaborator in . vcf format