def get_all_event_names(self):
"""
Return all event names in current samples dir.
"""
all_event_names = []
for curr_fname in self.all_filenames:
if curr_fname.endswith(".miso"):
# It's a regular .miso plain text file
event_name = \
get_event_name(curr_fname,
use_compressed_map=self.compressed_ids_to_genes)
# Record event name and its mapping to a .miso file
all_event_names.append(event_name)
self.event_names_to_fnames[event_name] = curr_fname
elif miso_db.is_miso_db_fname(curr_fname):
# It's a MISO database file, so load all the event
# names in that file
curr_db = \
miso_db.MISODatabase(curr_fname,
comp_to_uncomp=self.compressed_ids_to_genes)
# Record event name and its mapping to the chromosome's
# .miso_db file
for curr_event_name in curr_db.get_all_event_names():
curr_event_name = str(curr_event_name)
event_name_to_use = curr_event_name
# If we're given a mapping of compressed IDs, use the
# mapping to get the uncompressed event name
if self.compressed_ids_to_genes is not None:
# The internal database representation of compressed
# index databases are compressed IDs, so if the
# ID is uncompressed it must be converted to a
# compressed one.
if not misc_utils.is_compressed_name(curr_event_name):
event_name_to_use = \
str(curr_db.uncomp_to_comp[curr_event_name])
all_event_names.append(event_name_to_use)
self.event_names_to_fnames[event_name_to_use] = curr_fname
return all_event_names
def get_all_event_names(self):
"""
Return all event names in current samples dir.
"""
all_event_names = []
for curr_fname in self.all_filenames:
if curr_fname.endswith(".miso"):
# It's a regular .miso plain text file
event_name = \
get_event_name(curr_fname,
use_compressed_map=self.compressed_ids_to_genes)
# Record event name and its mapping to a .miso file
all_event_names.append(event_name)
self.event_names_to_fnames[event_name] = curr_fname
elif miso_db.is_miso_db_fname(curr_fname):
# It's a MISO database file, so load all the event
# names in that file
curr_db = \
miso_db.MISODatabase(curr_fname,
comp_to_uncomp=self.compressed_ids_to_genes)
# Record event name and its mapping to the chromosome's
# .miso_db file
for curr_event_name in curr_db.get_all_event_names():
curr_event_name = str(curr_event_name)
event_name_to_use = curr_event_name
# If we're given a mapping of compressed IDs, use the
# mapping to get the uncompressed event name
if self.compressed_ids_to_genes is not None:
# The internal database representation of compressed
# index databases are compressed IDs, so if the
# ID is uncompressed it must be converted to a
# compressed one.
if not misc_utils.is_compressed_name(curr_event_name):
event_name_to_use = \
str(curr_db.uncomp_to_comp[curr_event_name])
all_event_names.append(event_name_to_use)
self.event_names_to_fnames[event_name_to_use] = curr_fname
return all_event_names
def get_event_samples(self, event_name):
"""
Get the samples information for the given event by name.
"""
samples = None
if event_name not in self.event_names_to_fnames:
return None
event_fname = self.event_names_to_fnames[event_name]
if event_fname.endswith(".miso"):
# Get event from plain text .miso file
f = open(event_fname, "r")
samples = load_samples(f)
f.close()
elif miso_db.is_miso_db_fname(event_fname):
# Get event from miso_db file
curr_db = \
miso_db.MISODatabase(event_fname,
comp_to_uncomp=self.compressed_ids_to_genes)
event_data = curr_db.get_event_data_as_stream(event_name)
samples = load_samples(event_data)
if samples is None:
print "WARNING: Could not parse event %s samples" % (event_name)
return samples
def get_event_samples(self, event_name):
"""
Get the samples information for the given event by name.
"""
samples = None
if event_name not in self.event_names_to_fnames:
return None
event_fname = self.event_names_to_fnames[event_name]
if event_fname.endswith(".miso"):
# Get event from plain text .miso file
f = open(event_fname, "r")
samples = load_samples(f)
f.close()
elif miso_db.is_miso_db_fname(event_fname):
# Get event from miso_db file
curr_db = \
miso_db.MISODatabase(event_fname,
comp_to_uncomp=self.compressed_ids_to_genes)
event_data = curr_db.get_event_data_as_stream(event_name)
samples = load_samples(event_data)
if samples is None:
print "WARNING: Could not parse event %s samples" %(event_name)
return samples
