def index(request):
file_object = file_store.models.get_file_object(
"/Users/isytchev/Sites/tdf/"
"TCGA-AG-4007-01A-01D-1115-02_101122_SN177_0123_B20APUABXX_s_5.rg"
".sorted.chr21.bam.tdf")
tdf_file = tdf_module.TDFFile(file_object)
tdf_file.cache()
for track_name in tdf_file.get_track_names():
print(track_name)
for data_set_name in tdf_file.get_data_set_names():
print(data_set_name)
window_function = ""
if len(data_set_name.split("/")) == 4:
window_function = data_set_name.split("/")[3]
data_set = tdf_file.get_data_set(
data_set_name.split("/")[1],
data_set_name.split("/")[2], window_function)
data_set.read()
print("Tile Count: " + str(len(data_set.tile_index)))
print("Tile Width: " + str(data_set.tile_width))
print(data_set)
tile = data_set.get_tile(0)
print(tile)
tile = data_set.get_tile(1)
print(tile)
tile = data_set.get_tile(2)
print(tile)
tile = data_set.get_tile(3)
print(tile)
tile = data_set.get_tile(4)
print(tile)
tile = data_set.get_tile(5)
print(tile)
tile = data_set.get_tile(6)
print(tile)
tile = data_set.get_tile(7)
print(tile)
profile = tdf_file.get_profile("chr21",
"z0", ["mean"],
start_location=13591070,
end_location=14845362)
file_object.close()
return HttpResponse(json.dumps(profile), mimetype='application/json')
def cache_tdf(request, uuid, refresh=False):
try:
file_store_item = FileStoreItem.objects.get(uuid=uuid)
except (FileStoreItem.DoesNotExist,
FileStoreItem.MultipleObjectsReturned) as e:
logger.error("Couldn't properly fetch FileStoreItem: %s", e)
else:
if not _is_cached_tdf_file(request.session, uuid):
logger.debug("Caching file: %s ...", uuid)
tdf = tdf_module.TDFFile(file_store_item.get_file_object())
tdf.cache()
_cache_tdf_file(request.session, uuid, tdf)
else:
logger.debug("Retrieved file: %s ...", uuid)
tdf = _get_tdf_file_from_cache(request.session, uuid)
if not _is_cached_tdf_data_set_information(request.session,
uuid) or refresh:
logger.debug("Caching data set information: %s ...", uuid)
for data_set_name in tdf.get_data_set_names():
# decompose data set name
components = tdf.decompose_data_set_name(data_set_name)
data_set = tdf.get_data_set(components["sequence_name"],
components["zoom_level"],
components["window_function"])
data_set_information = {
"data_set_name": data_set_name,
"tile_width": data_set.tile_width,
"tile_count": str(len(data_set.tile_index))
}
_cache_tdf_data_set_information(request.session, uuid,
components,
data_set_information)
else:
logger.debug(
"%s data set information is cached and refresh not "
"requested", uuid)
return HttpResponse(json.dumps(
_get_tdf_data_set_information_from_cache(request.session, uuid),
sort_keys=True,
indent=4),
content_type='application/json')
def get_profile(self, zoom, seq, window, start, end):
"""Calculates and returns a profile from TDF file.
:param seq: Sequence name.
:type seq: str.
:param zoom: Zoom level.
:type zoom: int.
:param window: Window function.
:type window: str.
:param start: Start position.
:type start: int.
:param end: End position.
:type end: int.
:returns: JSON
"""
with self.get_file_object() as file_object:
tdf_file = tdf_module.TDFFile(file_object)
tdf_file.cache()
profile = tdf_file.get_profile(seq, zoom, ["mean"], start, end)
return json.dumps(profile)
def cache_tdf(request, uuid, refresh=False):
# TODO: call asynchronously
file_store_item = file_store.tasks.read(uuid)
if not _is_cached_tdf_file(request.session, uuid):
print("Caching file " + str(uuid) + " ...")
tdf = tdf_module.TDFFile(file_store_item.get_file_object())
tdf.cache()
_cache_tdf_file(request.session, uuid, tdf)
else:
print("Retrieved file " + str(uuid) + " ...")
tdf = _get_tdf_file_from_cache(request.session, uuid)
if not _is_cached_tdf_data_set_information(request.session,
uuid) or refresh:
print("Caching data set information " + str(uuid) + " ...")
for data_set_name in tdf.get_data_set_names():
# decompose data set name
components = tdf.decompose_data_set_name(data_set_name)
data_set = tdf.get_data_set(components["sequence_name"],
components["zoom_level"],
components["window_function"])
data_set_information = {
"data_set_name": data_set_name,
"tile_width": data_set.tile_width,
"tile_count": str(len(data_set.tile_index))
}
_cache_tdf_data_set_information(request.session, uuid, components,
data_set_information)
else:
print(
str(uuid) +
" data set information is cached and refresh not requested")
return HttpResponse(simplejson.dumps(
_get_tdf_data_set_information_from_cache(request.session, uuid),
sort_keys=True,
indent=4),
mimetype='application/json')