def get_painting_params(request):
source = helpers.check_source(request.GET.get('source', None))
resolution = helpers.check_resolution(request.GET.get('resolution', None))
chisq_cutoff = helpers.check_float(request.GET.get('chisq', None))
if None in (source, resolution, chisq_cutoff):
return http.HttpResponseBadRequest()
cursor = connections['default'].dict_cursor()
info = {}
query = '''
SELECT * FROM interpretome_ancestry.%s_%s_frequencies
WHERE chisq > %s
ORDER BY chromosome, position ASC
''' % (source, resolution, chisq_cutoff)
cursor.execute(query)
chromosomes = {}
for res in cursor.fetchall():
if res['chromosome'] not in chromosomes:
chromosomes[res['chromosome']] = []
chromosomes[res['chromosome']].append(res)
query = '''
SELECT chromosome, rel_length, rel_centromere, length
FROM interpretome_ancestry.chrom_info
ORDER BY chromosome;
'''
cursor.execute(query)
chrom_info = []
for res in cursor.fetchall():
chrom_info.append( [res['rel_length'], res['rel_centromere'], res['length']] )
response = {'chromosomes':chromosomes, 'chrom_info':chrom_info}
return http.HttpResponse(simplejson.dumps(response), 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 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 set_volume():
respone = volumizer.setVolume(check_float(request, params.VALUE))
if respone == None:
return send_error(error_codes.INVALID_VALUE, "Invalid volume value. Only 0 - 100")
respone.update({"code" : error_codes.SUCCESFULL_QUERY})
vol = respone['config']['milli']
playlistThreader.setVolume(vol)
trackThreader.setVolume(vol)
return jsonify(respone)
def get_volume():
value = check_float(request, params.VALUE)
if value != None and value != "":
vol_response = volumizer.setVolume(value)
if vol_response != None:
vol = vol_response['config']['milli']
playlistThreader.setVolume(vol)
trackThreader.setVolume(vol)
respone = volumizer.getJSON()
respone.update({"code" : error_codes.SUCCESFULL_QUERY})
return jsonify(respone)
def get_painting_params(request):
source = helpers.check_source(request.GET.get('source', None))
resolution = helpers.check_resolution(request.GET.get('resolution', None))
chisq_cutoff = helpers.check_float(request.GET.get('chisq', None))
if None in (source, resolution, chisq_cutoff):
return http.HttpResponseBadRequest()
cursor = connections['default'].dict_cursor()
info = {}
query = '''
SELECT * FROM interpretome_ancestry.%s_%s_frequencies
WHERE chisq > %s
ORDER BY chromosome, position ASC
''' % (source, resolution, chisq_cutoff)
cursor.execute(query)
chromosomes = {}
for res in cursor.fetchall():
if res['chromosome'] not in chromosomes:
chromosomes[res['chromosome']] = []
chromosomes[res['chromosome']].append(res)
query = '''
SELECT chromosome, rel_length, rel_centromere, length
FROM interpretome_ancestry.chrom_info
ORDER BY chromosome;
'''
cursor.execute(query)
chrom_info = []
for res in cursor.fetchall():
chrom_info.append(
[res['rel_length'], res['rel_centromere'], res['length']])
response = {'chromosomes': chromosomes, 'chrom_info': chrom_info}
return http.HttpResponse(simplejson.dumps(response),
mimetype="application/json")
