def loci(request):
chrom = request.GET.get('chrom', False)
loop_list = request.GET.get('loop-list', False)
# Get relative loci
(loci_rel,
chroms) = get_intra_chr_loops_from_looplist(path.join('data', loop_list),
chrom)
loci_rel_chroms = np.column_stack(
(chroms[:, 0], loci_rel[:, 0:2], chroms[:, 1], loci_rel[:, 2:4]))
# Create results
results = {'loci': rel_loci_2_obj(loci_rel_chroms)}
return JsonResponse(results)
def fragments_by_chr(request):
chrom = request.GET.get('chrom', False)
cooler_file = request.GET.get('cooler', False)
loop_list = request.GET.get('loop-list', False)
if cooler_file:
if cooler_file.endswith('.cool'):
cooler_file = path.join('data', cooler_file)
else:
try:
cooler_file = Tileset.objects.get(
uuid=cooler_file).datafile.path
except AttributeError:
return JsonResponse({
'error': 'Cooler file not in database',
},
status=500)
else:
return JsonResponse({
'error': 'Cooler file not specified',
},
status=500)
try:
measures = request.GET.getlist('measures', [])
except ValueError:
measures = []
try:
zoomout_level = int(request.GET.get('zoomout-level', -1))
except ValueError:
zoomout_level = -1
try:
limit = int(request.GET.get('limit', -1))
except ValueError:
limit = -1
try:
precision = int(request.GET.get('precision', False))
except ValueError:
precision = False
try:
no_cache = bool(request.GET.get('no-cache', False))
except ValueError:
no_cache = False
try:
for_config = bool(request.GET.get('for-config', False))
except ValueError:
for_config = False
# Get a unique string for the URL query string
uuid = hashlib.md5('-'.join([
cooler_file, chrom, loop_list,
str(limit),
str(precision),
str(zoomout_level)
])).hexdigest()
# Check if something is cached
if not no_cache:
try:
results = rdb.get('frag_by_chrom_%s' % uuid)
if results:
return JsonResponse(pickle.loads(results))
except:
pass
# Get relative loci
try:
(loci_rel, chroms) = get_intra_chr_loops_from_looplist(
path.join('data', loop_list), chrom)
except Exception as e:
return JsonResponse(
{
'error': 'Could not retrieve loci.',
'error_message': str(e)
},
status=500)
# Convert to chromosome-relative loci list
loci_rel_chroms = np.column_stack(
(chroms[:, 0], loci_rel[:, 0:2], chroms[:, 1], loci_rel[:, 2:4]))
if limit > 0:
loci_rel_chroms = loci_rel_chroms[:limit]
# Get fragments
try:
matrices = get_frag_by_loc(cooler_file,
loci_rel_chroms,
zoomout_level=zoomout_level)
except Exception as e:
return JsonResponse(
{
'error': 'Could not retrieve fragments.',
'error_message': str(e)
},
status=500)
if precision > 0:
matrices = np.around(matrices, decimals=precision)
fragments = []
loci_struct = rel_loci_2_obj(loci_rel_chroms)
# Check supported measures
measures_applied = []
for measure in measures:
if measure in SUPPORTED_MEASURES:
measures_applied.append(measure)
i = 0
for matrix in matrices:
measures_values = []
for measure in measures:
if measure == 'distance-to-diagonal':
measures_values.append(calc_measure_dtd(
matrix, loci_struct[i]))
if measure == 'size':
measures_values.append(
calc_measure_size(matrix, loci_struct[i]))
if measure == 'noise':
measures_values.append(calc_measure_noise(matrix))
if measure == 'sharpness':
measures_values.append(calc_measure_sharpness(matrix))
frag_obj = {
# 'matrix': matrix.tolist()
}
frag_obj.update(loci_struct[i])
frag_obj.update({"measures": measures_values})
fragments.append(frag_obj)
i += 1
# Create results
results = {
'count': matrices.shape[0],
'dims': matrices.shape[1],
'fragments': fragments,
'measures': measures_applied,
'relativeLoci': True,
'zoomoutLevel': zoomout_level
}
if for_config:
results['fragmentsHeader'] = [
'chrom1', 'start1', 'end1', 'strand1', 'chrom2', 'start2', 'end2',
'strand2'
] + measures_applied
fragments_arr = []
for fragment in fragments:
tmp = [
fragment['chrom1'],
fragment['start1'],
fragment['end1'],
fragment['strand1'],
fragment['chrom2'],
fragment['start2'],
fragment['end2'],
fragment['strand2'],
] + fragment['measures']
fragments_arr.append(tmp)
results['fragments'] = fragments_arr
# Cache results for 30 mins
try:
rdb.set('frag_by_chrom_%s' % uuid, pickle.dumps(results), 60 * 30)
except Exception as ex:
# error caching a tile
# log the error and carry forward, this isn't critical
logger.warn(ex)
return JsonResponse(results)
