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 submit(request):
request_dict = request.GET.copy()
try:
exercise = request_dict.pop('exercise')[0]
except KeyError:
return http.HttpResponseBadRequest()
cursor = connections['default'].dict_cursor()
if exercise in ('butte_diabetes', 'selection', 'assimes_cad', 'neandertal',
'eqtl', 'snyder_binding', 'mignot_narcolepsy', 'longevity',
'kim_aging'):
population = helpers.check_population(
request_dict.pop('population')[0])
cursor.execute('SELECT MAX(sid) FROM interpretome_exercises.unified;')
sid = cursor.fetchone().values()[0] + 1
statements = []
for k, v in request_dict.items():
string = "('%s', '%s', '%s', '%s', %d)" % (helpers.sanitize(
k), helpers.sanitize(v), population, exercise, int(sid))
statements.append(string)
query = '''
INSERT INTO interpretome_exercises.unified (`key`, `value`, population, exercise, sid)
VALUES %s;''' % ', '.join(statements)
cursor.execute(query)
return http.HttpResponse()
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 get_rare_variants(request):
population = helpers.check_population(request.GET.get('population', None))
cutoff = helpers.check_float(request.GET.get('cutoff', None))
if None in (population, cutoff):
return http.HttpResponseBadRequest()
query = '''SELECT rsid, refallele, otherallele, otherallele_freq
FROM var_hapmap.snp_frequencies_%s
WHERE otherallele_freq <= %s''' % (population.lower(), cutoff)
cursor = connections['default'].dict_cursor()
cursor.execute(query)
return http.HttpResponse(simplejson.dumps(cursor.fetchall()), mimetype = "application/json")
def get_rare_variants(request):
population = helpers.check_population(request.GET.get('population', None))
cutoff = helpers.check_float(request.GET.get('cutoff', None))
if None in (population, cutoff):
return http.HttpResponseBadRequest()
query = '''SELECT rsid, refallele, otherallele, otherallele_freq
FROM var_hapmap.snp_frequencies_%s
WHERE otherallele_freq <= %s''' % (population.lower(), cutoff)
cursor = connections['default'].dict_cursor()
cursor.execute(query)
return http.HttpResponse(simplejson.dumps(cursor.fetchall()),
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_gwas_catalog(request):
population = helpers.check_population(request.GET.get('population', None))
if population is None:
return http.HttpResponseBadRequest()
studies = get_possible_studies(population)
like_string = "%' or `initial_sample_size` like '%".join(studies)
query = '''
SELECT pubmedid, link, disease_trait, initial_sample_size, reported_genes,
or_or_beta, strongest_snp, risk_allele, p_value
FROM interpretome_clinical.gwas_catalog
WHERE initial_sample_size LIKE '%%%s%%'
ORDER BY disease_trait
''' % like_string
cursor = connections['default'].dict_cursor()
cursor.execute(query)
snps = cursor.fetchall()
return http.HttpResponse(simplejson.dumps(snps), 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_gwas_catalog(request):
population = helpers.check_population(request.GET.get('population', None))
if population is None:
return http.HttpResponseBadRequest()
studies = get_possible_studies(population)
like_string = "%' or `initial_sample_size` like '%".join(studies)
query = '''
SELECT pubmedid, link, disease_trait, initial_sample_size, reported_genes,
or_or_beta, strongest_snp, risk_allele, p_value
FROM interpretome_clinical.gwas_catalog
WHERE initial_sample_size LIKE '%%%s%%'
ORDER BY disease_trait
''' % like_string
cursor = connections['default'].dict_cursor()
cursor.execute(query)
snps = cursor.fetchall()
return http.HttpResponse(simplejson.dumps(snps),
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 submit(request):
request_dict = request.GET.copy()
try:
exercise = request_dict.pop('exercise')[0]
except KeyError:
return http.HttpResponseBadRequest()
cursor = connections['default'].dict_cursor()
if exercise in (
'butte_diabetes', 'selection', 'assimes_cad', 'neandertal', 'eqtl',
'snyder_binding', 'mignot_narcolepsy', 'longevity', 'kim_aging'
):
population = helpers.check_population(request_dict.pop('population')[0])
cursor.execute('SELECT MAX(sid) FROM interpretome_exercises.unified;')
sid = cursor.fetchone().values()[0] + 1
statements = []
for k, v in request_dict.items():
string = "('%s', '%s', '%s', '%s', %d)" % (helpers.sanitize(k), helpers.sanitize(v), population, exercise, int(sid))
statements.append(string)
query = '''
INSERT INTO interpretome_exercises.unified (`key`, `value`, population, exercise, sid)
VALUES %s;''' % ', '.join(statements)
cursor.execute(query)
return http.HttpResponse()
