def process(self, params={}):
self._MANAGERS = {
'variation': variation_components.DataManager(),
'treatment': treatment_components.DataManager(),
'trait': trait_components.DataManager(),
'publication': publication_components.DataManager(),
'gene': gene_components.DataManager(),
'exon': exon_components.DataManager(),
'disease': disease_components.DataManager(),
'chromosome': chromosome_components.DataManager(),
'drug': drug_components.DataManager(),
}
print "[x] RECEIVING DATA"
credentials = pika.PlainCredentials(settings.RABBITMQ_USER,
settings.RABBITMQ_PASS)
connection = pika.BlockingConnection(
pika.ConnectionParameters(settings.RABBITMQ_HOST,
settings.RABBITMQ_PORT, '/',
credentials))
channel = connection.channel()
channel.queue_declare(queue=os.environ.get('GENODATA_QUEUE'))
print "[*] Waiting for data. To exit press CTRL+C"
channel.basic_consume(self.consume,
queue=os.environ.get('GENODATA_QUEUE'),
no_ack=True)
channel.start_consuming()
def process(self, params={}):
fields = [
'1000-genomes', 'allele_string', 'chromosome', 'genename',
'vcf_RSPOS'
]
print '[***] Starting'
# Reset this field
Variation.objects.filter(is_good_quality=True).update(
is_good_quality=False)
variation_manager = variation_components.DataManager()
isDone = False
start = 0
while not isDone:
end = start + 5000
# print 'start: %s, end: %s' % (start, end)
records = Variation.objects.all()[start:end]
start = end + 1
if records.count() <= 0:
isDone = True
is_good_quality = False
ids = []
for var in records:
count = 0
data = variation_manager.get(var.code)
for i in fields:
if i in data and data[i]['value'] != None:
count += 1
if count == len(fields):
ids.append(var.id)
# Update database
Variation.objects.filter(pk__in=ids).update(is_good_quality=True)
print '[***] %s is good quality ---- DONE' % (len(ids))
def process(self, params={}):
_managers = {
'variation': variation_components.DataManager(),
'treatment': treatment_components.DataManager(),
'trait': trait_components.DataManager(),
'publication': publication_components.DataManager(),
'gene': gene_components.DataManager(),
'exon': exon_components.DataManager(),
'disease': disease_components.DataManager(),
'chromosome': chromosome_components.DataManager(),
'drug': drug_components.DataManager(),
}
_filename = params.get('_FILE')
if _filename:
print "[x] RECEIVING DATA"
try:
with gzip.open('{}'.format(_filename), 'r') as f:
for line in f:
data = json.loads(line)
if len(data) >= 5:
field_not_exist = []
print "Entity: %s, Record: %s, Field: %s, Value: %s" % (
data[1], data[2], data[3], data[4])
try:
if _managers.get(data[1], None) != None:
field_not_exist = _managers[data[1]].put(
data[2], {data[3]: data[4]},
source=data[0])
except Exception as e:
pass
if field_not_exist:
print "[**] Fields are not exist in Genodata: %s" % (
field_not_exist)
except Exception as e:
raise e
else:
print "[Error] Expected gzip text file to import, empty given"
def process(self, params={}):
# DECLARE VARIABLE
NAME_QUEUE = 'user-variation'
RABBITMQ_HOST = settings.RABBITMQ_HOST
RABBITMQ_PORT = int(settings.RABBITMQ_PORT)
# Starting
print "[x] Publish data to rabbitmq"
##########################
## Variation
isDone = False
start = 0
manager = components.DataManager()
while not isDone:
end = start + 5000
variation = Variation.objects.filter(
is_good_quality=True)[start:end]
start = end + 1
if variation.count() <= 0:
isDone = True
x = []
for var in variation:
y = {'version': '0.1', 'rsnumber': var.code}
try:
data = manager.get(var.code)
arr_disease = []
y['chromosome'] = data['chromosome']['value']
y['position'] = data['vcf_RSPOS']['value']
y['science_filter'] = ''
y['genes'] = data['genename']['value']
if data['publications']['value']:
y['publications'] = data['publications']['value']
if data['gwas-effects']['value']:
y['effects'] = []
for eff in data['gwas-effects']['value']:
effe = {}
effe['genotype'] = eff['genotype']
effe['odd_ratio'] = eff['odd_ratio']
effe['effect'] = eff['effect']
y['effects'].append(effe)
# disease
if data['disgenet-diseases']['value']:
arr_disease.extend(data['disgenet-diseases']['value'])
if data['gwas-diseases']['value']:
for k in data['gwas-diseases']['value']:
arr_disease.append({
'disease':
k.get('disease', ''),
'pubmedid':
k.get('pmid', ''),
'sentence':
k.get('sentence', '')
})
if len(arr_disease) > 0:
y['diseases'] = arr_disease
except Exception as e:
pass
x.append(y)
# Publish rabbitMQ
self.publish_to_queue(x, NAME_QUEUE, RABBITMQ_HOST, RABBITMQ_PORT)
print "[***] DONE variation"
def process(self, params={}):
# DECLARE VARIABLE
SEQUENCE_QUEUE = 'sequence-viewer-variation'
RABBITMQ_HOST = settings.RABBITMQ_HOST
RABBITMQ_PORT = int(settings.RABBITMQ_PORT)
# Starting
print "[x] Publish data to rabbitmq"
##########################
## Variation
isDone = False
start = 0
variation_manager = variation_components.DataManager()
fields = ['chromosome', 'genename', 'vcf_RSPOS']
while not isDone:
end = start + 5000
variation = Variation.objects.all()[start:end]
start = end + 1
if variation.count() <= 0:
isDone = True
x = []
for var in variation:
count = 0
y = ['variation', var.code]
arr_disease = []
data = variation_manager.get(var.code)
for i in fields:
if i in data and data[i]['value'] != None:
count += 1
if count == len(fields):
# disease
if data['disgenet-diseases']['value']:
arr_disease.extend(data['disgenet-diseases']['value'])
if data['gwas-diseases']['value']:
for k in data['gwas-diseases']['value']:
arr_disease.append({
'disease':
k.get('disease', ''),
'pubmedid':
k.get('pmid', ''),
'sentence':
k.get('sentence', '')
})
y.append({
'chromosome': data['chromosome']['value'],
'genename': data['genename']['value'],
'position': data['vcf_RSPOS']['value'],
'associated_diseases': arr_disease
})
x.append(y)
if len(x) > 0:
print "[***] starting publish to rabbitMQ"
# Publish rabbitMQ
self.publish_to_queue(x, SEQUENCE_QUEUE, RABBITMQ_HOST,
RABBITMQ_PORT)
print "[***] DONE variation"
def process(self, params = {}):
# DECLARE VARIABLE
GENOME_QUEUE = 'genome-browser-variation'
RABBITMQ_HOST = settings.RABBITMQ_HOST
RABBITMQ_PORT = int(settings.RABBITMQ_PORT)
# Starting
print "[x] Publish data to rabbitmq"
##########################
## Variation
isDone = False
start = 0
manager = variation_components.DataManager()
while not isDone:
end = start + 5000
variation = Variation.objects.filter(is_good_quality=True)[start:end]
start = end + 1
if variation.count() <= 0:
isDone = True
x = []
for var in variation:
y = {'version': '0.1', 'rsnumber': var.code}
try:
data = manager.get(var.code)
# print 'code: %s' % (code)
arr_disease = []
asso_disease = []
asso_pub = []
y['core_attributes'] = {
'chromosome': data['chromosome'].get('value', ''),
'position': data['vcf_RSPOS'].get('value', ''),
'allele_string': data['allele_string'].get('value', ''),
'synonyms': data['synonyms'].get('value', '')
}
y['genename'] = data['genename']['value']
y['1000-genomes'] = data['1000-genomes']['value']
if data['publications']['value']:
y['publications'] = data['publications']['value']
if data['gwas-effects']['value']:
y['effects'] = []
# y['effects'] = data['gwas-effects']['value']
for eff in data['gwas-effects']['value']:
effe = eff
if eff.get('effect', ''):
effe['risk'] = 'Increased risk of %s' % (eff['effect'])
else:
effe['risk'] = ''
if eff.get('initial', ''):
effe['evidences'] = 'Initial: %s' % (eff['initial'])
if eff.get('replication', ''):
effe['evidences'] += ', replication: %s' % (eff['replication'])
else:
effe['evidences'] = ''
y['effects'].append(effe)
if data['genotype_frequency']['value']:
y['genotype_frequency'] = data['genotype_frequency']['value']
# disease
if data['disgenet-diseases']['value']:
arr_disease.extend(data['disgenet-diseases']['value'])
rs = [ item['disease'] for item in data['disgenet-diseases']['value'] ]
asso_disease.extend(rs)
if data['gwas-diseases']['value']:
for k in data['gwas-diseases']['value']:
arr_disease.append({
'disease': k.get('disease',''),
'pubmedid': k.get('pmid',''),
'sentence': k.get('sentence', '')
})
rs = [ item['disease'] for item in data['gwas-diseases']['value'] ]
asso_disease.extend(rs)
if len(arr_disease) > 0:
y['disgenet-diseases'] = arr_disease
if len(asso_disease) > 0:
y['associated_diseases'] = asso_disease
# publication
if data['publications']['value']:
for k in data['publications']['value']:
asso_pub.append({
'pmid': k.get('pmid', ''),
'title': k.get('title','')
})
if data['gwas-publications']['value']:
asso_pub.extend(data['gwas-publications']['value'])
if len(asso_pub) > 0:
y['associated_publications'] = asso_pub
except Exception as e:
pass
x.append(y)
# Publish rabbitMQ
self.publish_to_queue(x, GENOME_QUEUE, RABBITMQ_HOST, RABBITMQ_PORT)
print "[***] DONE variation"
def process(self, params={}):
keys = [
'synonyms', 'name', 'is_somatic', 'minor_allele_frequency',
'evidence_attributes', 'ancestral_allele', 'minor_allele_count',
'clinic_significance', 'minor_allele', 'effects', 'chromosome',
'publications', 'genotype_frequency', 'hgvs', 'allele',
'allele_frequency', 'associated_disease', 'attribute', 'var_type',
'var_property', 'var_disease', 'reversed', 'gwas-effects',
'1000-genomes', 'disgenet-diseases', 'genename', 'allele_string',
'consequence_types', 'ensembl-id', 'name', 'vcf_U5', 'vcf_ASS',
'vcf_DSS', 'vcf_INT', 'vcf_R3', 'vcf_R5', 'vcf_OTH', 'vcf_CFL',
'vcf_ASP', 'vcf_MUT', 'vcf_VLD', 'vcf_G5A', 'vcf_G5', 'vcf_HD',
'vcf_GNO', 'vcf_KGPhase1', 'vcf_KGPhase3', 'vcf_CDA', 'vcf_LSD',
'vcf_MTP', 'vcf_OM', 'vcf_NOC', 'vcf_WTD', 'vcf_NOV', 'vcf_CAF',
'vcf_COMMON', 'vcf_CLNHGVS', 'vcf_CLNALLE', 'vcf_CLNSRC',
'vcf_CLNORIGIN', 'vcf_CLNSRCID', 'vcf_CLNSIG', 'vcf_CLNDSDB',
'vcf_CLNDSDBID', 'vcf_CLNDBN', 'vcf_CLNREVSTAT', 'vcf_CLNACC',
'vcf_REF', 'vcf_ALT', 'vcf_RS', 'vcf_RSPOS', 'vcf_RV', 'vcf_VP',
'vcf_GENEINFO', 'vcf_dbSNPBuildID', 'vcf_SAO', 'vcf_SSR',
'vcf_WGT', 'vcf_VC', 'vcf_PM', 'vcf_TPA', 'vcf_PMC', 'vcf_S3D',
'vcf_SLO', 'vcf_NSF', 'vcf_NSM', 'vcf_NSN', 'vcf_REF', 'vcf_SYN',
'vcf_U3'
]
rsnumbers = []
manager = variation_components.DataManager()
for r in Variation.objects.all():
try:
vol = manager.get(r.code)
if vol is None:
continue
for k in vol.keys():
if k in keys and vol[k].get('value', '') not in ['', None]:
print "[Value]", vol[k].get('value', '')
rsnumbers.append(r.code)
except Exception as e:
pass
print "[RSNUMBER] Top 10"
x = Counter(rsnumbers)
print sorted(x.items(), key=operator.itemgetter(0))[:10]
keys = [
'geneid', 'chromosome', 'start', 'end', 'num_exon',
'protein_product', 'description', 'associated_disease', 'synonyms',
'publications', 'havana_gene', 'biotype', 'is_reversed',
'ctdbase-diseases', 'disgenet-diseases', 'id', 'name'
]
genes = []
manager = gene_components.DataManager()
for r in Gene.objects.all():
try:
vol = manager.get(r.code)
if vol is None:
continue
for k in vol.keys():
if k in keys and vol[k].get('value', '') not in ['', None]:
print "[Value]", vol[k].get('value', '')
genes.append(r.code)
except Exception as e:
pass
print "[GENE] Top 10"
x = Counter(genes)
print sorted(x.items(), key=operator.itemgetter(0))[:10]