def impute(request):
'''Impute one or more SNPs.
dbsnp will be one or more dbSNP identifiers (only rsIDs), separated by commas.
'''
dbsnps = helpers.check_dbsnp_array(request.REQUEST.get('dbsnps', None))
user_dbsnps = helpers.check_dbsnp_array(
request.REQUEST.get('user_dbsnps', None))
population = helpers.check_population(
request.REQUEST.get('population', None))
if None in (dbsnps, population, user_dbsnps):
return http.HttpResponseBadRequest()
cursor = connections['default'].dict_cursor()
phases = {}
for index, dbsnp in enumerate(dbsnps):
query_snp_in_hapmap = helpers.get_individuals(cursor, dbsnp,
population)
anchor_snp_in_hapmap = helpers.get_individuals(cursor,
user_dbsnps[index],
population)
phase = helpers.get_best_phases(query_snp_in_hapmap,
anchor_snp_in_hapmap)
phase['user_snp'] = user_dbsnps[index]
phases[dbsnp] = phase
return http.HttpResponse(simplejson.dumps(phases),
mimetype="application/json")
def get_damaging_info(request):
dbsnps = helpers.check_dbsnp_array(request.GET.get('snps', None))
output = {}
if dbsnps is None:
return http.HttpResponseBadRequest()
cursor = connections['default'].dict_cursor()
for dbsnp in dbsnps:
query = '''
SELECT chrom FROM %s
WHERE rsid=%s
''' % (dbsnp_table, dbsnp)
cursor.execute(query)
chrom = cursor.fetchone()
if chrom is not None and chrom['chrom'] is not None:
query = '''
SELECT * FROM public_coding.dbNSFP1_3_chr%s
WHERE unisnp_ids LIKE "%%rs%s%%"
''' % (chrom['chrom'], dbsnp)
cursor.execute(query)
data = cursor.fetchone()
if data is not None:
output[dbsnp] = data
return http.HttpResponse(simplejson.dumps(output),
mimetype="application/json")
def get_snps_on_map(request):
dbsnps = helpers.check_dbsnp_array(request.GET.get('dbsnps', None))
cursor = connections['default'].dict_cursor()
output = {}
for dbsnp in dbsnps:
query = 'select alfred_uid from interpretome_ancestry.alfred_variant_info where rs_number ="rs%s"' % dbsnp
output[dbsnp] = cursor.execute(query)
return http.HttpResponse(simplejson.dumps(output), mimetype = "application/json")
def get_snps_on_map(request):
dbsnps = helpers.check_dbsnp_array(request.GET.get('dbsnps', None))
cursor = connections['default'].dict_cursor()
output = {}
for dbsnp in dbsnps:
query = 'select alfred_uid from interpretome_ancestry.alfred_variant_info where rs_number ="rs%s"' % dbsnp
output[dbsnp] = cursor.execute(query)
return http.HttpResponse(simplejson.dumps(output),
mimetype="application/json")
def linked(request):
dbsnps = helpers.check_dbsnp_array(request.REQUEST.get('dbsnps', None))
population = helpers.check_population(
request.REQUEST.get('population', None))
ld_cutoff = helpers.check_float(request.REQUEST.get('ld_cutoff', None))
if None in (dbsnps, population, ld_cutoff):
return http.HttpResponseBadRequest()
cursor = connections['default'].dict_cursor()
results = {}
for dbsnp in dbsnps:
query = '''
SELECT *
FROM var_hapmap.hapmap_phased_%s
WHERE dbSNP = %s;
''' % (population, dbsnp)
cursor.execute(query)
hapmap_result = cursor.fetchone()
query = '''
SELECT dbSNP1, dbSNP2, R_square
FROM var_ld_data.ld_%s
WHERE dbSNP1 = %d OR dbSNP2 = %d
AND R_square >= %s
ORDER BY R_square DESC;
''' % (population, dbsnp, dbsnp, ld_cutoff)
cursor.execute(query)
raw_result = cursor.fetchall()
if hapmap_result is None or raw_result is None:
results[dbsnp] = []
continue
result = []
for entry in raw_result:
if entry['dbSNP1'] == dbsnp:
other_dbsnp = entry['dbSNP2']
else:
other_dbsnp = entry['dbSNP1']
query = '''
SELECT *
FROM var_hapmap.hapmap_phased_%s
WHERE dbSNP = %s;
''' % (population, other_dbsnp)
cursor.execute(query)
if cursor.fetchone() is not None:
result.append(entry)
results[dbsnp] = result
return http.HttpResponse(simplejson.dumps(results),
mimetype='application/json')
def linked(request):
dbsnps = helpers.check_dbsnp_array(request.REQUEST.get('dbsnps', None))
population = helpers.check_population(request.REQUEST.get('population', None))
ld_cutoff = helpers.check_float(request.REQUEST.get('ld_cutoff', None))
if None in (dbsnps, population, ld_cutoff):
return http.HttpResponseBadRequest()
cursor = connections['default'].dict_cursor()
results = {}
for dbsnp in dbsnps:
query = '''
SELECT *
FROM var_hapmap.hapmap_phased_%s
WHERE dbSNP = %s;
''' % (population, dbsnp)
cursor.execute(query)
hapmap_result = cursor.fetchone()
query = '''
SELECT dbSNP1, dbSNP2, R_square
FROM var_ld_data.ld_%s
WHERE dbSNP1 = %d OR dbSNP2 = %d
AND R_square >= %s
ORDER BY R_square DESC;
''' % (population, dbsnp, dbsnp, ld_cutoff)
cursor.execute(query)
raw_result = cursor.fetchall()
if hapmap_result is None or raw_result is None:
results[dbsnp] = []
continue
result = []
for entry in raw_result:
if entry['dbSNP1'] == dbsnp:
other_dbsnp = entry['dbSNP2']
else:
other_dbsnp = entry['dbSNP1']
query = '''
SELECT *
FROM var_hapmap.hapmap_phased_%s
WHERE dbSNP = %s;
''' % (population, other_dbsnp)
cursor.execute(query)
if cursor.fetchone() is not None:
result.append(entry)
results[dbsnp] = result
return http.HttpResponse(simplejson.dumps(results), mimetype = 'application/json')
def impute(request):
'''Impute one or more SNPs.
dbsnp will be one or more dbSNP identifiers (only rsIDs), separated by commas.
'''
dbsnps = helpers.check_dbsnp_array(request.REQUEST.get('dbsnps', None))
user_dbsnps = helpers.check_dbsnp_array(request.REQUEST.get('user_dbsnps', None))
population = helpers.check_population(request.REQUEST.get('population', None))
if None in (dbsnps, population, user_dbsnps):
return http.HttpResponseBadRequest()
cursor = connections['default'].dict_cursor()
phases = {}
for index, dbsnp in enumerate(dbsnps):
query_snp_in_hapmap = helpers.get_individuals(cursor, dbsnp, population)
anchor_snp_in_hapmap = helpers.get_individuals(cursor, user_dbsnps[index], population)
phase = helpers.get_best_phases(query_snp_in_hapmap, anchor_snp_in_hapmap)
phase['user_snp'] = user_dbsnps[index]
phases[dbsnp] = phase
return http.HttpResponse(simplejson.dumps(phases), mimetype = "application/json")
def get_chrom_pos(request):
dbsnps = helpers.check_dbsnp_array(request.GET.get('snps', None))
if dbsnps is None:
return http.HttpResponseBadRequest()
info = {}
for dbsnp in dbsnps:
query = '''
SELECT chrom, chromstart, chromend FROM %s
WHERE rsid=%s
''' % (dbsnp_table, dbsnp)
cursor = connections['default'].dict_cursor()
cursor.execute(query)
data = cursor.fetchone()
info[dbsnp] = data
return http.HttpResponse(simplejson.dumps(info), mimetype = "application/json")
def get_allele_frequencies(request):
dbsnps = helpers.check_dbsnp_array(request.GET.get('snps', None))
population = helpers.check_population(request.GET.get('population', None))
if None in (population, dbsnps):
return http.HttpResponseBadRequest()
cursor = connections['default'].dict_cursor()
frequencies = {}
for dbsnp in dbsnps:
query = '''
SELECT refallele, refallele_freq, otherallele, otherallele_freq FROM var_hapmap.allele_freqs_%s
WHERE rsid=%s
''' % (population, dbsnp)
cursor.execute(query)
data = cursor.fetchone()
frequencies[dbsnp] = data
return http.HttpResponse(simplejson.dumps(frequencies), mimetype = "application/json")
def get_chrom_pos(request):
dbsnps = helpers.check_dbsnp_array(request.GET.get('snps', None))
if dbsnps is None:
return http.HttpResponseBadRequest()
info = {}
for dbsnp in dbsnps:
query = '''
SELECT chrom, chromstart, chromend FROM %s
WHERE rsid=%s
''' % (dbsnp_table, dbsnp)
cursor = connections['default'].dict_cursor()
cursor.execute(query)
data = cursor.fetchone()
info[dbsnp] = data
return http.HttpResponse(simplejson.dumps(info),
mimetype="application/json")
def get_reference_alleles(request):
dbsnps = helpers.check_dbsnp_array(request.GET.get('snps', None))
references = {}
if dbsnps is None:
return http.HttpResponseBadRequest()
for dbsnp in dbsnps:
query = '''
SELECT strand, refncbi FROM %s
WHERE rsid=%s
''' % (dbsnp_table, dbsnp)
cursor = connections['default'].dict_cursor()
cursor.execute(query)
data = cursor.fetchone()
if data is not None:
references[dbsnp] = data['refncbi']
return http.HttpResponse(simplejson.dumps(references), mimetype = "application/json")
def get_allele_frequencies(request):
dbsnps = helpers.check_dbsnp_array(request.GET.get('snps', None))
population = helpers.check_population(request.GET.get('population', None))
if None in (population, dbsnps):
return http.HttpResponseBadRequest()
cursor = connections['default'].dict_cursor()
frequencies = {}
for dbsnp in dbsnps:
query = '''
SELECT refallele, refallele_freq, otherallele, otherallele_freq FROM var_hapmap.allele_freqs_%s
WHERE rsid=%s
''' % (population, dbsnp)
cursor.execute(query)
data = cursor.fetchone()
frequencies[dbsnp] = data
return http.HttpResponse(simplejson.dumps(frequencies),
mimetype="application/json")
def get_reference_alleles(request):
dbsnps = helpers.check_dbsnp_array(request.GET.get('snps', None))
references = {}
if dbsnps is None:
return http.HttpResponseBadRequest()
for dbsnp in dbsnps:
query = '''
SELECT strand, refncbi FROM %s
WHERE rsid=%s
''' % (dbsnp_table, dbsnp)
cursor = connections['default'].dict_cursor()
cursor.execute(query)
data = cursor.fetchone()
if data is not None:
references[dbsnp] = data['refncbi']
return http.HttpResponse(simplejson.dumps(references),
mimetype="application/json")
def get_damaging_info(request):
dbsnps = helpers.check_dbsnp_array(request.GET.get('snps', None))
output = {}
if dbsnps is None:
return http.HttpResponseBadRequest()
cursor = connections['default'].dict_cursor()
for dbsnp in dbsnps:
query = '''
SELECT chrom FROM %s
WHERE rsid=%s
''' % (dbsnp_table, dbsnp)
cursor.execute(query)
chrom = cursor.fetchone()
if chrom is not None and chrom['chrom'] is not None:
query = '''
SELECT * FROM public_coding.dbNSFP1_3_chr%s
WHERE unisnp_ids LIKE "%%rs%s%%"
''' % (chrom['chrom'], dbsnp)
cursor.execute(query)
data = cursor.fetchone()
if data is not None:
output[dbsnp] = data
return http.HttpResponse(simplejson.dumps(output), mimetype = "application/json")
