def parse_locus_list_items(request_json):
raw_items = request_json.get('rawItems')
if not raw_items:
return None, None, None
invalid_items = []
intervals = []
gene_ids = set()
gene_symbols = set()
for item in raw_items.replace(',', ' ').replace('\t', '<TAB>').split():
interval_match = re.match(
'(?P<chrom>\w+):(?P<start>\d+)-(?P<end>\d+)(%(?P<offset>(\d+)))?',
item)
if not interval_match:
interval_match = re.match(
'(?P<chrom>\w+)<TAB>(?P<start>\d+)<TAB>(?P<end>\d+)', item)
if interval_match:
interval = interval_match.groupdict()
try:
interval['chrom'] = interval['chrom'].lstrip('chr')
interval['start'] = int(interval['start'])
interval['end'] = int(interval['end'])
if interval.get('offset'):
interval['offset'] = int(interval['offset']) / 100
if interval['start'] > interval['end']:
raise ValueError
get_xpos(interval['chrom'], interval['start'])
intervals.append(interval)
except (KeyError, ValueError):
invalid_items.append('chr{chrom}:{start}-{end}'.format(
chrom=interval.get('chrom'),
start=interval.get('start'),
end=interval.get('end')))
elif item.upper().startswith('ENSG'):
gene_ids.add(item.replace('<TAB>', ''))
else:
gene_symbols.add(item.replace('<TAB>', ''))
gene_symbols_to_ids = get_gene_ids_for_gene_symbols(gene_symbols)
invalid_items += [
symbol for symbol in gene_symbols
if not gene_symbols_to_ids.get(symbol)
]
gene_ids.update({
gene_ids[0]
for gene_ids in gene_symbols_to_ids.values() if len(gene_ids)
})
genes_by_id = get_genes(list(gene_ids)) if gene_ids else {}
invalid_items += [
gene_id for gene_id in gene_ids if not genes_by_id.get(gene_id)
]
return genes_by_id, intervals, invalid_items
def _get_saved_variants(variants, families):
if not variants:
return {}, {}
prefetch_related_objects(families, 'project')
hg37_family_guids = {
family.guid
for family in families
if family.project.genome_version == GENOME_VERSION_GRCh37
}
variant_q = Q()
variants_by_id = {}
for variant in variants:
variants_by_id[_get_variant_key(**variant)] = variant
variant_q |= Q(xpos_start=variant['xpos'],
ref=variant['ref'],
alt=variant['alt'],
family__guid__in=variant['familyGuids'])
if variant[
'liftedOverGenomeVersion'] == GENOME_VERSION_GRCh37 and hg37_family_guids:
variant_hg37_families = [
family_guid for family_guid in variant['familyGuids']
if family_guid in hg37_family_guids
]
if variant_hg37_families:
lifted_xpos = get_xpos(variant['liftedOverChrom'],
variant['liftedOverPos'])
variant_q |= Q(xpos_start=lifted_xpos,
ref=variant['ref'],
alt=variant['alt'],
family__guid__in=variant_hg37_families)
variants_by_id[_get_variant_key(
xpos=lifted_xpos,
ref=variant['ref'],
alt=variant['alt'],
genomeVersion=variant['liftedOverGenomeVersion']
)] = variant
saved_variants = SavedVariant.objects.filter(variant_q)
saved_variants_json = get_json_for_saved_variants(saved_variants,
add_tags=True,
add_details=True)
saved_variants_by_guid = {}
variants_to_saved_variants = {}
for saved_variant in saved_variants_json:
family_guids = saved_variant['familyGuids']
searched_variant = variants_by_id[_get_variant_key(**saved_variant)]
saved_variant.update(searched_variant)
# For saved variants only use family it was saved for, not all families in search
saved_variant['familyGuids'] = family_guids
saved_variants_by_guid[saved_variant['variantGuid']] = saved_variant
if searched_variant['variantId'] not in variants_to_saved_variants:
variants_to_saved_variants[searched_variant['variantId']] = {}
for family_guid in family_guids:
variants_to_saved_variants[searched_variant['variantId']][
family_guid] = saved_variant['variantGuid']
return saved_variants_by_guid, variants_to_saved_variants
def _parse_variant_items(search_json):
raw_items = search_json.get('rawVariantItems')
if not raw_items:
return None, None, None
invalid_items = []
variant_ids = []
rs_ids = []
for item in raw_items.replace(',', ' ').split():
if item.startswith('rs'):
rs_ids.append(item)
else:
try:
chrom, pos, _, _ = EsSearch.parse_variant_id(item)
get_xpos(chrom, pos)
variant_ids.append(item.lstrip('chr'))
except (KeyError, ValueError):
invalid_items.append(item)
return rs_ids, variant_ids, invalid_items
def _get_saved_variants(variants, families, include_discovery_tags=False):
variants = _flatten_variants(variants)
prefetch_related_objects(families, 'project')
hg37_family_guids = {family.guid for family in families if family.project.genome_version == GENOME_VERSION_GRCh37}
variant_q = Q()
variants_by_id = {}
for variant in variants:
variants_by_id[get_variant_key(**variant)] = variant
variant_q |= Q(variant_id=variant['variantId'], family__guid__in=variant['familyGuids'])
if variant['liftedOverGenomeVersion'] == GENOME_VERSION_GRCh37 and hg37_family_guids:
variant_hg37_families = [family_guid for family_guid in variant['familyGuids'] if family_guid in hg37_family_guids]
if variant_hg37_families:
lifted_xpos = get_xpos(variant['liftedOverChrom'], variant['liftedOverPos'])
variant_q |= Q(xpos=lifted_xpos, ref=variant['ref'], alt=variant['alt'], family__guid__in=variant_hg37_families)
variants_by_id[get_variant_key(
xpos=lifted_xpos, ref=variant['ref'], alt=variant['alt'], genomeVersion=variant['liftedOverGenomeVersion']
)] = variant
saved_variants = SavedVariant.objects.filter(variant_q)
json = get_json_for_saved_variants_with_tags(saved_variants, add_details=True)
discovery_tags = {}
if include_discovery_tags:
discovery_tags, discovery_response = get_json_for_discovery_tags(variants)
json.update(discovery_response)
variants_to_saved_variants = {}
for saved_variant in json['savedVariantsByGuid'].values():
family_guids = saved_variant['familyGuids']
searched_variant = variants_by_id.get(get_variant_key(**saved_variant))
if not searched_variant:
# This can occur when an hg38 family has a saved variant that did not successfully lift from hg37
continue
saved_variant.update(searched_variant)
# For saved variants only use family it was saved for, not all families in search
saved_variant['familyGuids'] = family_guids
json['savedVariantsByGuid'][saved_variant['variantGuid']] = saved_variant
if searched_variant['variantId'] not in variants_to_saved_variants:
variants_to_saved_variants[searched_variant['variantId']] = {}
for family_guid in family_guids:
variants_to_saved_variants[searched_variant['variantId']][family_guid] = saved_variant['variantGuid']
for variant_id, tags in discovery_tags.items():
searched_variant = variants_by_id.get(variant_id)
if searched_variant:
if not searched_variant.get('discoveryTags'):
searched_variant['discoveryTags'] = []
searched_variant['discoveryTags'] += [
tag for tag in tags if tag['savedVariant']['familyGuid'] not in searched_variant['familyGuids']]
return json, variants_to_saved_variants
def _location_filter(genes, intervals, location_filter):
q = None
if intervals:
q = _build_or_filter('range', [{
'xpos': {
'gte': get_xpos(interval['chrom'], interval['start']),
'lte': get_xpos(interval['chrom'], interval['end'])
}
} for interval in intervals])
if genes:
gene_q = Q('terms', geneIds=genes.keys())
if q:
q |= gene_q
else:
q = gene_q
if location_filter.get('excludeLocations'):
return ~q
else:
return q
def _location_filter(genes, intervals, location_filter):
q = None
if intervals:
q = _build_or_filter('range', [{
'xpos': {
'gte': get_xpos(interval['chrom'], interval['start']),
'lte': get_xpos(interval['chrom'], interval['end'])
}
} for interval in intervals])
if genes:
gene_q = Q('terms', geneIds=genes.keys())
if q:
q |= gene_q
else:
q = gene_q
if location_filter.get('excludeLocations'):
return ~q
else:
return q
def _parse_list_items(request_json):
requested_items = (request_json.get('parsedItems') or {}).get('items') or []
existing_gene_ids = set()
new_gene_symbols = set()
new_gene_ids = set()
existing_interval_guids = set()
new_intervals = []
invalid_items = []
for item in requested_items:
if item.get('locusListIntervalGuid'):
existing_interval_guids.add(item.get('locusListIntervalGuid'))
elif item.get('geneId'):
if item.get('symbol'):
existing_gene_ids.add(item.get('geneId'))
else:
new_gene_ids.add(item.get('geneId'))
elif item.get('symbol'):
new_gene_symbols.add(item.get('symbol'))
else:
try:
item['start'] = int(item['start'])
item['end'] = int(item['end'])
if item['start'] > item['end']:
raise ValueError
get_xpos(item['chrom'], int(item['start']))
new_intervals.append(item)
except (KeyError, ValueError):
invalid_items.append('chr{chrom}:{start}-{end}'.format(
chrom=item.get('chrom', '?'), start=item.get('start', '?'), end=item.get('end', '?')
))
gene_symbols_to_ids = get_gene_ids_for_gene_symbols(new_gene_symbols)
invalid_items += [symbol for symbol in new_gene_symbols if not gene_symbols_to_ids.get(symbol)]
invalid_items += [symbol for symbol in new_gene_symbols if len(gene_symbols_to_ids.get(symbol, [])) > 1]
new_genes = get_genes([gene_ids[0] for gene_ids in gene_symbols_to_ids.values() if len(gene_ids) == 1] + list(new_gene_ids),
add_dbnsfp=True, add_omim=True, add_constraints=True)
invalid_items += [gene_id for gene_id, gene in new_genes.items() if not gene]
new_genes = {gene_id: gene for gene_id, gene in new_genes.items() if gene}
return new_genes, existing_gene_ids, new_intervals, existing_interval_guids, invalid_items
def _get_parsed_variant_args(variant_json, family):
if 'xpos' not in variant_json:
variant_json['xpos'] = get_xpos(variant_json['chrom'], variant_json['pos'])
xpos = variant_json['xpos']
ref = variant_json['ref']
alt = variant_json['alt']
var_length = variant_json['pos_end'] - variant_json['pos'] if 'pos_end' in variant_json else len(ref) - 1
return {
'xpos': xpos,
'xpos_start': xpos,
'xpos_end': xpos + var_length,
'ref': ref,
'alt': alt,
'family': family,
}
def _get_parsed_variant_args(variant_json, family):
if 'xpos' not in variant_json:
variant_json['xpos'] = get_xpos(variant_json['chrom'], variant_json['pos'])
xpos = variant_json['xpos']
ref = variant_json.get('ref')
alt = variant_json.get('alt')
var_length = variant_json['end'] - variant_json['pos'] if 'end' in variant_json else len(ref) - 1
return {
'xpos': xpos,
'xpos_end': xpos + var_length,
'ref': ref,
'alt': alt,
'family': family,
'variant_id': variant_json['variantId']
}
def create_saved_variant_handler(request):
variant_json = json.loads(request.body)
family_guid = variant_json.pop('familyGuid')
non_variant_json = {
k: variant_json.pop(k, None)
for k in [
'searchHash', 'tags', 'functionalData', 'notes', 'note',
'submitToClinvar'
]
}
family = Family.objects.get(guid=family_guid)
check_permissions(family.project, request.user, CAN_VIEW)
if 'xpos' not in variant_json:
variant_json['xpos'] = get_xpos(variant_json['chrom'],
variant_json['pos'])
xpos = variant_json['xpos']
ref = variant_json['ref']
alt = variant_json['alt']
var_length = variant_json['pos_end'] - variant_json[
'pos'] if 'pos_end' in variant_json else len(ref) - 1
saved_variant = SavedVariant.objects.create(
xpos=xpos,
xpos_start=xpos,
xpos_end=xpos + var_length,
ref=ref,
alt=alt,
family=family,
saved_variant_json=variant_json)
if non_variant_json.get('note'):
_create_variant_note(saved_variant, non_variant_json, request.user)
elif non_variant_json.get('tags'):
_create_new_tags(saved_variant, non_variant_json, request.user)
variant_json.update(
get_json_for_saved_variant(saved_variant, add_tags=True))
return create_json_response({
'savedVariantsByGuid': {
saved_variant.guid: variant_json
},
})
def test_get_xpos(self):
self.assertRaises(ValueError, lambda: get_xpos('chrUnknown', 1))
self.assertRaises(ValueError, lambda: get_xpos('chr22', 0))
self.assertRaises(ValueError, lambda: get_xpos('chr22', 1e9))
self.assertEqual(get_xpos('1', 10), 1e9 + 10)
self.assertEqual(get_xpos('chr1', 10), 1e9 + 10)
self.assertEqual(get_xpos('22', 10), 22 * 1e9 + 10)
self.assertEqual(get_xpos('X', 10), 23 * 1e9 + 10)
self.assertEqual(get_xpos('chrX', 10), 23 * 1e9 + 10)
self.assertEqual(get_xpos('Y', 10), 24 * 1e9 + 10)
self.assertEqual(get_xpos('chrY', 10), 24 * 1e9 + 10)
self.assertEqual(get_xpos('M', 10), 25 * 1e9 + 10)
self.assertEqual(get_xpos('chrM', 10), 25 * 1e9 + 10)
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})
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 _get_saved_variants(variants, families, include_discovery_tags=False):
if not variants:
return {}, {}
variants = _flatten_variants(variants)
prefetch_related_objects(families, 'project')
hg37_family_guids = {
family.guid
for family in families
if family.project.genome_version == GENOME_VERSION_GRCh37
}
variant_q = Q()
discovery_variant_q = Q()
variants_by_id = {}
for variant in variants:
variants_by_id[_get_variant_key(**variant)] = variant
variant_q |= Q(xpos_start=variant['xpos'],
ref=variant['ref'],
alt=variant['alt'],
family__guid__in=variant['familyGuids'])
discovery_variant_q |= Q(
Q(xpos_start=variant['xpos'],
ref=variant['ref'],
alt=variant['alt'])
& ~Q(family__guid__in=variant['familyGuids']))
if variant[
'liftedOverGenomeVersion'] == GENOME_VERSION_GRCh37 and hg37_family_guids:
variant_hg37_families = [
family_guid for family_guid in variant['familyGuids']
if family_guid in hg37_family_guids
]
if variant_hg37_families:
lifted_xpos = get_xpos(variant['liftedOverChrom'],
variant['liftedOverPos'])
variant_q |= Q(xpos_start=lifted_xpos,
ref=variant['ref'],
alt=variant['alt'],
family__guid__in=variant_hg37_families)
variants_by_id[_get_variant_key(
xpos=lifted_xpos,
ref=variant['ref'],
alt=variant['alt'],
genomeVersion=variant['liftedOverGenomeVersion']
)] = variant
saved_variants = SavedVariant.objects.filter(variant_q)
json = get_json_for_saved_variants_with_tags(saved_variants,
add_details=True)
variants_to_saved_variants = {}
for saved_variant in json['savedVariantsByGuid'].values():
family_guids = saved_variant['familyGuids']
searched_variant = variants_by_id.get(
_get_variant_key(**saved_variant))
if not searched_variant:
# This can occur when an hg38 family has a saved variant that did not successfully lift from hg37
continue
saved_variant.update(searched_variant)
# For saved variants only use family it was saved for, not all families in search
saved_variant['familyGuids'] = family_guids
json['savedVariantsByGuid'][
saved_variant['variantGuid']] = saved_variant
if searched_variant['variantId'] not in variants_to_saved_variants:
variants_to_saved_variants[searched_variant['variantId']] = {}
for family_guid in family_guids:
variants_to_saved_variants[searched_variant['variantId']][
family_guid] = saved_variant['variantGuid']
if include_discovery_tags:
discovery_tags = get_json_for_variant_tags(
VariantTag.objects.filter(
variant_tag_type__category='CMG Discovery Tags',
saved_variants__in=SavedVariant.objects.filter(
discovery_variant_q)),
include_variant_details=True)
if discovery_tags:
family_guids = set()
for tag in discovery_tags:
for variant in tag['variants']:
family_guids.update(variant['familyGuids'])
families_by_guid = {
f.guid: f
for f in Family.objects.filter(
guid__in=family_guids).prefetch_related('project')
}
for tag in discovery_tags:
for variant in tag.pop('variants'):
variant_family = families_by_guid[variant['familyGuids']
[0]]
searched_variant = variants_by_id.get(
_get_variant_key(genomeVersion=variant_family.project.
genome_version,
**variant))
if searched_variant:
if not searched_variant.get('discoveryTags'):
searched_variant['discoveryTags'] = []
tag_json = {
'savedVariant': {
'variantGuid': variant['variantGuid'],
'familyGuid': variant_family.guid,
'projectGuid': variant_family.project.guid,
}
}
tag_json.update(tag)
searched_variant['discoveryTags'].append(tag_json)
json['familiesByGuid'] = {
f['familyGuid']: f
for f in _get_json_for_families(families_by_guid.values())
}
return json, variants_to_saved_variants
def test_get_xpos(self):
self.assertRaises(ValueError, lambda: get_xpos('chrUnknown', 1))
self.assertRaises(ValueError, lambda: get_xpos('chr22', 0))
self.assertRaises(ValueError, lambda: get_xpos('chr22', 1e9))
self.assertEqual(get_xpos('1', 10), 1e9 + 10)
self.assertEqual(get_xpos('chr1', 10), 1e9 + 10)
self.assertEqual(get_xpos('22', 10), 22*1e9 + 10)
self.assertEqual(get_xpos('X', 10), 23*1e9 + 10)
self.assertEqual(get_xpos('chrX', 10), 23*1e9 + 10)
self.assertEqual(get_xpos('Y', 10), 24*1e9 + 10)
self.assertEqual(get_xpos('chrY', 10), 24*1e9 + 10)
self.assertEqual(get_xpos('M', 10), 25*1e9 + 10)
self.assertEqual(get_xpos('chrM', 10), 25*1e9 + 10)
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)))
