def exercise(request):
'''Get SNP data for an exercise.'''
exercise = request.GET.get('exercise', None)
# Defaults
fields = '*'
where_clause = ''
db = 'interpretome_exercises'
table = exercise
# Supported exercises
exercises = [
'ashley_cad', 'tang_ancestry', 'altman_pgx', 'butte_diabetes',
'assimes_cad', 'snyder_binding', 'class_writeups', 'mignot_narcolepsy',
'kim_aging', 'eqtl', 'longevity', 'selection', 'neandertal'
]
if exercise not in exercises:
return http.HttpResponseBadRequest()
# Set query parameters
if exercise == 'longevity':
where_clause = 'ORDER BY log10_bf DESC'
elif exercise == 'selection':
pop = request.REQUEST.get('population')
where_clause = "WHERE pop = '%s' AND selected IS NOT NULL" % pop
query = '''SELECT %(fields)s FROM %(db)s.%(table)s %(where)s
''' % {
'fields': fields,
'db': db,
'table': table,
'where': where_clause
}
# Get type of snp_dict
cursor = connections['default'].dict_cursor()
cursor.execute(query)
snps = {}
if exercise in ('snyder_binding'):
result = cursor.fetchall()
snps['snps'] = helpers.create_multi_snp_dict(result)
else:
result = cursor.fetchall()
snps['snps'] = helpers.create_snp_dict(result)
# Post-processing
if exercise == 'longevity':
snps['sorted_dbsnps'] = [e['dbsnp'] for e in result]
return http.HttpResponse(simplejson.dumps(snps),
mimetype='application/json')
def exercise(request):
'''Get SNP data for an exercise.'''
exercise = request.GET.get('exercise', None)
# Defaults
fields = '*'
where_clause = ''
db = 'interpretome_exercises'
table = exercise
# Supported exercises
exercises = ['ashley_cad', 'tang_ancestry', 'altman_pgx', 'butte_diabetes',
'assimes_cad', 'snyder_binding', 'class_writeups',
'mignot_narcolepsy', 'kim_aging',
'eqtl', 'longevity', 'selection', 'neandertal']
if exercise not in exercises:
return http.HttpResponseBadRequest()
# Set query parameters
if exercise == 'longevity':
where_clause = 'ORDER BY log10_bf DESC'
elif exercise == 'selection':
pop = request.REQUEST.get('population')
where_clause = "WHERE pop = '%s' AND selected IS NOT NULL" % pop
query = '''SELECT %(fields)s FROM %(db)s.%(table)s %(where)s
''' % {'fields': fields, 'db': db, 'table': table, 'where': where_clause}
# Get type of snp_dict
cursor = connections['default'].dict_cursor()
cursor.execute(query)
snps = {}
if exercise in ('snyder_binding'):
result = cursor.fetchall()
snps['snps'] = helpers.create_multi_snp_dict(result)
else:
result = cursor.fetchall()
snps['snps'] = helpers.create_snp_dict(result)
# Post-processing
if exercise == 'longevity':
snps['sorted_dbsnps'] = [e['dbsnp'] for e in result]
return http.HttpResponse(simplejson.dumps(snps), mimetype = 'application/json')
def get_individuals(request):
numsnps = helpers.check_int(request.GET.get('numsnps', None))
if numsnps is None:
return http.HttpResponseBadRequest()
individuals = helpers.sanitize(request.GET.get('individuals', None)).split(',')
individual_select = set()
for individual in individuals:
if individual == '210-2011-staff':
individual_select.update(['Konrad', 'Nick', 'Noah', 'Rob', 'Stuart'])
else:
individual_select.add(individual)
if len(individual_select) == 0:
return http.HttpResponseBadRequest()
cursor = connections['default'].dict_cursor()
query = '''
SELECT dbsnp, %s FROM interpretome_ancestry.similarity LIMIT %s;
''' % (",".join([str(i) for i in individual_select]), numsnps)
cursor.execute(query)
output = helpers.create_snp_dict(cursor.fetchall())
return http.HttpResponse(simplejson.dumps(output), mimetype = 'application/json')
def get_individuals(request):
numsnps = helpers.check_int(request.GET.get('numsnps', None))
if numsnps is None:
return http.HttpResponseBadRequest()
individuals = helpers.sanitize(request.GET.get('individuals',
None)).split(',')
individual_select = set()
for individual in individuals:
if individual == '210-2011-staff':
individual_select.update(
['Konrad', 'Nick', 'Noah', 'Rob', 'Stuart'])
else:
individual_select.add(individual)
if len(individual_select) == 0:
return http.HttpResponseBadRequest()
cursor = connections['default'].dict_cursor()
query = '''
SELECT dbsnp, %s FROM interpretome_ancestry.similarity LIMIT %s;
''' % (",".join([str(i) for i in individual_select]), numsnps)
cursor.execute(query)
output = helpers.create_snp_dict(cursor.fetchall())
return http.HttpResponse(simplejson.dumps(output),
mimetype='application/json')
