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, 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)
if json:
click.echo(dumps([var for var in variants]))
return
vcf_header = [
"##fileformat=VCFv4.2", "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"
]
for line in vcf_header:
click.echo(line)
#put variants in a dict to get unique ones
variant_string = ("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}")
for variant_obj in variants:
click.echo(
variant_string.format(
variant_obj['chromosome'], variant_obj['position'],
variant_obj['dbsnp_id'], variant_obj['reference'],
variant_obj['alternative'], variant_obj['quality'],
';'.join(variant_obj['filters']), '.'))
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(collaborator: str, document_id: str, case_id: str, json: bool):
"""Export causatives for a collaborator in .vcf format"""
LOG.info("Running scout export variants")
adapter = store
collaborator = collaborator or "cust000"
LOG.info("Use collaborator %s", collaborator)
if case_id:
case_obj = adapter.case(case_id)
if not case_obj:
LOG.info("Case %s does not exist", case_id)
raise click.Abort
variants = export_variants(adapter,
collaborator,
document_id=document_id,
case_id=case_id)
if json:
click.echo(
json_lib.dumps([var for var in variants], default=bson_handler))
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)