def data_for_heatmap(self, request):
""" Get hitmap data. Parameters need to be included in the filters. Check the FAQ for details on the filters."""
# Usage: chrom = indicate the chromosome(s) of interest ('all' or any chromosome),
# region_width = indicate the size of the bins for which to count hits,
# threshold = indicate the type of threshold to look at (FDR, Bonferroni, permutation or none, default='FDR')
# region = indicate a specific window in which to aggregate for, default = ('','') looks at entire chromosome
# maf = indicate a minimum maf (default=0)
# mac = indicate a minimum mac (default=0)
# Load studies from regular db
recompute = request.query_params.getlist('recompute')
if recompute == []:
# import requests
file_name = "%s/heatmap_data.json" % (settings.HDF5_FILE_PATH)
# url = 'https://gist.githubusercontent.com/mtog/95d29b45e0f58e5c11dc61818f4c57fb/raw/b5bf20b80d168e6d3a3a261e204c34a97c72ba5b/pre_loaded_heatmap_data.json'
# return Response(requests.get(url).json())
import json
with open(file_name) as data_file: # There seems to be a displaying problem when loading from file: the histograms are loaded and displayed twice
data = json.load(data_file)
return Response(data)
studies = Study.objects.all()
studies_data = []
for study in studies:
studies_data.append(
{'id': study.id, 'name': study.phenotype.name}) # For now only add phenotype name for shorted strings
# get the rest of the data
filters = dict()
# Get region params for zoomed regions...
filters['chrom'] = request.query_params.get('chromosome')
region = request.query_params.getlist('region')
filters['region']=(int(region[0]),int(region[1]))
filters['region_width'] = request.query_params.get('regionwidth')
results = elastic.get_gwas_overview_heatmap_data(filters, len(studies))
results['studies'] = studies_data
return Response(results)
def generate_hitmap_json():
studies = Study.objects.all()
studies_data = []
for study in studies:
studies_data.append(
{'id': study.id, 'name': study.phenotype.name}) # For now only add phenotype name for shorted strings
filters = dict()
results = elastic.get_gwas_overview_heatmap_data(filters)
results['studies'] = studies_data
file_name = "%s/heatmap_data.json" % (settings.HDF5_FILE_PATH)
with open(file_name, 'w') as out_file:
json.dump(results, out_file)
def generate_hitmap_json():
abs_filename = os.path.join(settings.HDF5_FILE_PATH,"heatmap_data.json")
if not _check_modifed(abs_filename):
logger.info('Hitmap already up2date. Skipping generation')
return
Path('%s.run' % abs_filename).touch()
studies = Study.objects.all()
studies_data = []
for study in studies:
studies_data.append(
{'id': study.id, 'name': study.phenotype.name}) # For now only add phenotype name for shorted strings
num_studies = len(studies)
filters = dict()
results = elastic.get_gwas_overview_heatmap_data(filters, num_studies)
results['studies'] = studies_data
with open('%s.tmp' % abs_filename, 'w') as out_file:
json.dump(results, out_file)
os.rename('%s.tmp' % abs_filename, abs_filename)
logger.info('Finished generating hitmap')