def _retrieve_saved_variants_json(project, variant_tuples):
xpos_ref_alt_tuples = []
xpos_ref_alt_family_tuples = []
family_id_to_guid = {}
for xpos, ref, alt, family in variant_tuples:
xpos_ref_alt_tuples.append((xpos, ref, alt))
xpos_ref_alt_family_tuples.append((xpos, ref, alt, family.family_id))
family_id_to_guid[family.family_id] = family.guid
families = project.family_set.filter(guid__in=family_id_to_guid.values())
return get_es_variants_for_variant_tuples(families, xpos_ref_alt_tuples)
def _retrieve_saved_variants_json(project, variant_tuples, create_if_missing=False):
xpos_ref_alt_tuples = []
xpos_ref_alt_family_tuples = []
family_id_to_guid = {}
for xpos, ref, alt, family in variant_tuples:
xpos_ref_alt_tuples.append((xpos, ref, alt))
xpos_ref_alt_family_tuples.append((xpos, ref, alt, family.family_id))
family_id_to_guid[family.family_id] = family.guid
try:
families = project.family_set.filter(guid__in=family_id_to_guid.values())
return get_es_variants_for_variant_tuples(families, xpos_ref_alt_tuples)
except InvalidIndexException:
return deprecated_retrieve_saved_variants_json(project, xpos_ref_alt_family_tuples, create_if_missing)
def _retrieve_saved_variants_json(project, variant_tuples, create_if_missing=False):
xpos_ref_alt_tuples = []
xpos_ref_alt_family_tuples = []
family_id_to_guid = {}
for xpos, ref, alt, family in variant_tuples:
xpos_ref_alt_tuples.append((xpos, ref, alt))
xpos_ref_alt_family_tuples.append((xpos, ref, alt, family.family_id))
family_id_to_guid[family.family_id] = family.guid
try:
families = project.family_set.filter(guid__in=family_id_to_guid.values())
return get_es_variants_for_variant_tuples(families, xpos_ref_alt_tuples)
except InvalidIndexException:
variants = _deprecated_retrieve_saved_variants_json(project, xpos_ref_alt_family_tuples, create_if_missing)
for var in variants:
var['familyGuids'] = [family_id_to_guid[var['extras']['family_id']]]
return variants
def handle(self, *args, **options):
"""transfer project"""
project_arg = options['project']
elasticsearch_index = options['es_index']
project = Project.objects.get(
Q(name=project_arg) | Q(guid=project_arg))
logger.info('Updating project genome version for {}'.format(
project.name))
# Validate the provided index
logger.info('Validating es index {}'.format(elasticsearch_index))
sample_ids, index_metadata = get_elasticsearch_index_samples(
elasticsearch_index)
validate_index_metadata(index_metadata,
project,
elasticsearch_index,
genome_version=GENOME_VERSION_GRCh38)
sample_type = index_metadata['sampleType']
dataset_path = index_metadata['sourceFilePath']
matched_sample_id_to_sample_record = match_sample_ids_to_sample_records(
project=project,
sample_ids=sample_ids,
sample_type=sample_type,
dataset_type=Sample.DATASET_TYPE_VARIANT_CALLS,
elasticsearch_index=elasticsearch_index,
sample_id_to_individual_id_mapping={},
)
unmatched_samples = set(sample_ids) - set(
matched_sample_id_to_sample_record.keys())
if len(unmatched_samples) > 0:
raise CommandError(
'Matches not found for ES sample ids: {}.'.format(
', '.join(unmatched_samples)))
prefetch_related_objects(matched_sample_id_to_sample_record.values(),
'individual__family')
included_families = {
sample.individual.family
for sample in matched_sample_id_to_sample_record.values()
}
missing_individuals = Individual.objects.filter(
family__in=included_families,
sample__is_active=True,
sample__dataset_type=Sample.DATASET_TYPE_VARIANT_CALLS,
).exclude(sample__in=matched_sample_id_to_sample_record.values()
).select_related('family')
missing_family_individuals = defaultdict(list)
for individual in missing_individuals:
missing_family_individuals[individual.family].append(individual)
if missing_family_individuals:
raise CommandError(
'The following families are included in the callset but are missing some family members: {}.'
.format(', '.join([
'{} ({})'.format(
family.family_id,
', '.join([i.individual_id for i in missing_indivs]))
for family, missing_indivs in
missing_family_individuals.items()
])))
# Get and clean up expected saved variants
saved_variant_models_by_guid = {
v.guid: v
for v in SavedVariant.objects.filter(family__project=project)
}
deleted_no_tags = set()
for guid, variant in saved_variant_models_by_guid.items():
if not (variant.varianttag_set.count()
or variant.variantnote_set.count()):
deleted_no_tags.add(guid)
if deleted_no_tags:
if raw_input(
'Do you want to delete the following {} saved variants with no tags (y/n)?: {} '
.format(len(deleted_no_tags),
', '.join(deleted_no_tags))) == 'y':
for guid in deleted_no_tags:
saved_variant_models_by_guid.pop(guid).delete()
logger.info('Deleted {} variants'.format(len(deleted_no_tags)))
expected_families = {
sv.family
for sv in saved_variant_models_by_guid.values()
}
missing_families = expected_families - included_families
if missing_families:
raise CommandError(
'The following families have saved variants but are missing from the callset: {}.'
.format(', '.join([f.family_id for f in missing_families])))
# Lift-over saved variants
_update_variant_samples(matched_sample_id_to_sample_record,
elasticsearch_index, dataset_path)
saved_variants = get_json_for_saved_variants(
saved_variant_models_by_guid.values(), add_details=True)
saved_variants_to_lift = [
v for v in saved_variants
if v['genomeVersion'] != GENOME_VERSION_GRCh38
]
num_already_lifted = len(saved_variants) - len(saved_variants_to_lift)
if num_already_lifted:
if raw_input(
'Found {} saved variants already on Hg38. Continue with liftover (y/n)? '
.format(num_already_lifted)) != 'y':
raise CommandError(
'Error: found {} saved variants already on Hg38'.format(
num_already_lifted))
logger.info(
'Lifting over {} variants (skipping {} that are already lifted)'.
format(len(saved_variants_to_lift), num_already_lifted))
liftover_to_38 = LiftOver('hg19', 'hg38')
hg37_to_hg38_xpos = {}
lift_failed = {}
for v in saved_variants_to_lift:
if not (hg37_to_hg38_xpos.get(v['xpos'])
or v['xpos'] in lift_failed):
hg38_coord = liftover_to_38.convert_coordinate(
'chr{}'.format(v['chrom'].lstrip('chr')), int(v['pos']))
if hg38_coord and hg38_coord[0]:
hg37_to_hg38_xpos[v['xpos']] = get_xpos(
hg38_coord[0][0], hg38_coord[0][1])
else:
lift_failed[v['xpos']] = v
if lift_failed:
if raw_input(
'Unable to lift over the following {} coordinates. Continue with update (y/n)?: {} '
.format(
len(lift_failed), ', '.join([
'{}:{}-{}-{} ({})'.format(
v['chrom'], v['pos'], v['ref'], v['alt'],
', '.join(v['familyGuids']))
for v in lift_failed.values()
]))) != 'y':
raise CommandError(
'Error: unable to lift over {} variants'.format(
len(lift_failed)))
saved_variants_map = defaultdict(list)
for v in saved_variants_to_lift:
if hg37_to_hg38_xpos.get(v['xpos']):
variant_model = saved_variant_models_by_guid[v['variantGuid']]
saved_variants_map[(hg37_to_hg38_xpos[v['xpos']], v['ref'],
v['alt'])].append(variant_model)
es_variants = get_es_variants_for_variant_tuples(
expected_families, saved_variants_map.keys())
missing_variants = set(
saved_variants_map.keys()) - {(v['xpos'], v['ref'], v['alt'])
for v in es_variants}
if missing_variants:
missing_variant_strings = []
for xpos, ref, alt in missing_variants:
var_id = '{}-{}-{}'.format(xpos, ref, alt)
for v in saved_variants_map[(xpos, ref, alt)]:
tags = v.varianttag_set.all()
notes = v.variantnote_set.all()
missing_variant_strings.append(
'{var_id} {family_id}: {tags} ({guid})'.format(
var_id=var_id,
family_id=v.family.family_id,
guid=v.guid,
tags=', '.join([
tag.variant_tag_type.name for tag in tags
]) if tags else 'No Tags; {}'.format('; '.join(
[note.note for note in notes]))))
if raw_input(
'Unable to find the following {} variants in the index. Continue with update (y/n)?:\n{}\n'
.format(len(missing_variants),
'\n'.join(missing_variant_strings))) != 'y':
raise CommandError(
'Error: unable to find {} lifted-over variants'.format(
len(missing_variants)))
logger.info('Successfully lifted over {} variants'.format(
len(es_variants)))
# Update saved variants
missing_family_count = 0
for var in es_variants:
saved_variant_models = saved_variants_map[(var['xpos'], var['ref'],
var['alt'])]
missing_saved_variants = [
v for v in saved_variant_models
if v.family.guid not in var['familyGuids']
]
if missing_saved_variants:
variant_id = '{}-{}-{}-{}'.format(var['chrom'], var['pos'],
var['ref'], var['alt'])
if raw_input(
('Variant {} (hg37: {}) not find for expected families {}. Continue with update (y/n)? '
.format(
variant_id, missing_saved_variants[0].xpos,
', '.join([
'{} ({})'.format(v.family.guid, v.guid)
for v in missing_saved_variants
])))) == 'y':
var = get_single_es_variant(
[v.family for v in saved_variant_models],
variant_id,
return_all_queried_families=True)
missing_family_count += len(missing_saved_variants)
else:
raise CommandError(
'Error: unable to find family data for lifted over variant'
)
for saved_variant in saved_variant_models:
saved_variant.xpos_start = var['xpos']
saved_variant.saved_variant_json = var
saved_variant.save()
logger.info('Successfully updated {} variants'.format(
len(es_variants)))
# Update project and sample data
update_model_from_json(project, {
'genome_version': GENOME_VERSION_GRCh38,
'has_new_search': True
})
update_xbrowse_vcfffiles(project, sample_type, elasticsearch_index,
dataset_path,
matched_sample_id_to_sample_record)
reset_cached_search_results(project)
logger.info('---Done---')
logger.info(
'Succesfully lifted over {} variants. Skipped {} failed variants. Family data not updated for {} variants'
.format(len(es_variants),
len(missing_variants) + len(lift_failed),
missing_family_count))
def handle(self, *args, **options):
"""transfer project"""
project_arg = options['project']
elasticsearch_index = options['es_index']
project = Project.objects.get(Q(name=project_arg) | Q(guid=project_arg))
logger.info('Updating project genome version for {}'.format(project.name))
# Validate the provided index
logger.info('Validating es index {}'.format(elasticsearch_index))
sample_ids, index_metadata = get_elasticsearch_index_samples(elasticsearch_index)
validate_index_metadata(index_metadata, project, elasticsearch_index, genome_version=GENOME_VERSION_GRCh38)
sample_type = index_metadata['sampleType']
dataset_path = index_metadata['sourceFilePath']
matched_sample_id_to_sample_record = match_sample_ids_to_sample_records(
project=project,
sample_ids=sample_ids,
sample_type=sample_type,
dataset_type=Sample.DATASET_TYPE_VARIANT_CALLS,
elasticsearch_index=elasticsearch_index,
sample_id_to_individual_id_mapping={},
)
unmatched_samples = set(sample_ids) - set(matched_sample_id_to_sample_record.keys())
if len(unmatched_samples) > 0:
raise Exception('Matches not found for ES sample ids: {}.'.format(', '.join(unmatched_samples)))
included_family_individuals = defaultdict(set)
individual_guids_by_id = {}
for sample in matched_sample_id_to_sample_record.values():
included_family_individuals[sample.individual.family].add(sample.individual.individual_id)
individual_guids_by_id[sample.individual.individual_id] = sample.individual.guid
missing_family_individuals = []
for family, individual_ids in included_family_individuals.items():
missing_indivs = family.individual_set.filter(
sample__sample_status=Sample.SAMPLE_STATUS_LOADED,
sample__dataset_type=Sample.DATASET_TYPE_VARIANT_CALLS
).exclude(individual_id__in=individual_ids)
if missing_indivs:
missing_family_individuals.append(
'{} ({})'.format(family.family_id, ', '.join([i.individual_id for i in missing_indivs]))
)
if missing_family_individuals:
raise Exception(
'The following families are included in the callset but are missing some family members: {}.'.format(
', '.join(missing_family_individuals)
))
# Get and clean up expected saved variants
saved_variant_models_by_guid = {v.guid: v for v in SavedVariant.objects.filter(project=project)}
deleted_no_family = set()
deleted_no_tags = set()
for guid, variant in saved_variant_models_by_guid.items():
if not variant.family:
deleted_no_family.add(guid)
elif not (variant.varianttag_set.count() or variant.variantnote_set.count()):
deleted_no_tags.add(guid)
if deleted_no_family:
if raw_input('Do you want to delete the following {} saved variants with no family (y/n)?: {} '.format(
len(deleted_no_family), ', '.join(deleted_no_family))) == 'y':
for guid in deleted_no_family:
saved_variant_models_by_guid.pop(guid).delete()
logger.info('Deleted {} variants'.format(len(deleted_no_family)))
if deleted_no_tags:
if raw_input('Do you want to delete the following {} saved variants with no tags (y/n)?: {} '.format(
len(deleted_no_tags), ', '.join(deleted_no_tags))) == 'y':
for guid in deleted_no_tags:
saved_variant_models_by_guid.pop(guid).delete()
logger.info('Deleted {} variants'.format(len(deleted_no_tags)))
expected_families = {sv.family for sv in saved_variant_models_by_guid.values()}
missing_families = expected_families - set(included_family_individuals.keys())
if missing_families:
raise Exception(
'The following families have saved variants but are missing from the callset: {}.'.format(
', '.join([f.family_id for f in missing_families])
))
# Lift-over saved variants
saved_variants = get_json_for_saved_variants(
saved_variant_models_by_guid.values(), add_details=True, project=project,
individual_guids_by_id=individual_guids_by_id)
saved_variants_to_lift = [v for v in saved_variants if v['genomeVersion'] != GENOME_VERSION_GRCh38]
num_already_lifted = len(saved_variants) - len(saved_variants_to_lift)
if num_already_lifted:
if raw_input('Found {} saved variants already on Hg38. Continue with liftover (y/n)?'.format(num_already_lifted)) != 'y':
raise Exception('Error: found {} saved variants already on Hg38'.format(num_already_lifted))
logger.info('Lifting over {} variants (skipping {} that are already lifted)'.format(
len(saved_variants_to_lift), num_already_lifted))
liftover_to_38 = LiftOver('hg19', 'hg38')
hg37_to_hg38_xpos = {}
lift_failed = set()
for v in saved_variants_to_lift:
if not (hg37_to_hg38_xpos.get(v['xpos']) or v['xpos'] in lift_failed):
hg38_coord = liftover_to_38.convert_coordinate('chr{}'.format(v['chrom'].lstrip('chr')), int(v['pos']))
if hg38_coord and hg38_coord[0]:
hg37_to_hg38_xpos[v['xpos']] = get_xpos(hg38_coord[0][0], hg38_coord[0][1])
else:
lift_failed.add(v['xpos'])
if lift_failed:
raise Exception(
'Unable to lift over the following {} coordinates: {}'.format(len(lift_failed), ', '.join(lift_failed)))
saved_variants_map = defaultdict(list)
for v in saved_variants_to_lift:
variant_model = saved_variant_models_by_guid[v['variantGuid']]
saved_variants_map[(hg37_to_hg38_xpos[v['xpos']], v['ref'], v['alt'])].append(variant_model)
es_variants = get_es_variants_for_variant_tuples(expected_families, saved_variants_map.keys())
missing_variants = set(saved_variants_map.keys()) - {(v['xpos'], v['ref'], v['alt']) for v in es_variants}
if missing_variants:
missing_variant_strings = ['{}-{}-{} ({})'.format(
xpos, ref, alt,
', '.join(['{}: {}'.format(v.family.family_id, v.guid) for v in saved_variants_map[(xpos, ref, alt)]]))
for xpos, ref, alt in missing_variants]
if raw_input('Unable to find the following {} variants in the index. Continue with update (y/n)?: {} '.format(
len(missing_variants), ', '.join(missing_variant_strings))) != 'y':
raise Exception('Error: unable to find {} lifted-over variants'.format(len(missing_variants)))
logger.info('Successfully lifted over {} variants'.format(len(es_variants)))
# Update saved variants
for var in es_variants:
saved_variant_models = saved_variants_map[(var['xpos'], var['ref'], var['alt'])]
missing_families = [v.family.guid for v in saved_variant_models if v.family.guid not in var['familyGuids']]
if missing_families:
raise Exception('Error with variant {}:{}-{}-{} not find for expected families {}; found in families {}'.format(
var['chrom'], var['pos'], var['ref'], var['alt'], ', '.join(missing_families), ', '.join(var['familyGuids'])
))
for saved_variant in saved_variant_models:
saved_variant.xpos_start = var['xpos']
saved_variant.saved_variant_json = json.dumps(var)
saved_variant.save()
logger.info('Successfully updated {} variants'.format(len(es_variants)))
# Update project and sample data
update_model_from_json(project, {'genome_version': GENOME_VERSION_GRCh38, 'has_new_search': True})
_update_samples(
matched_sample_id_to_sample_record, elasticsearch_index=elasticsearch_index, dataset_path=dataset_path
)
update_xbrowse_vcfffiles(
project, sample_type, elasticsearch_index, dataset_path, matched_sample_id_to_sample_record
)
reset_cached_search_results(project)
logger.info('---Done---')
logger.info('Succesfully lifted over {} variants. Skipped {} failed variants.'.format(
len(es_variants), len(missing_variants)))