def loaded_events_to_genes(self,
single_event_name=None,
read_len=None,
overhang_len=None):
"""
Parse the loaded set of events into gene structures. Map events to genes.
"""
if len(self.events) == 0:
raise Exception, "Must load events first before they can be converted to genes."
events_to_genes = {}
t1 = time.time()
if single_event_name:
# If given an event name, only parse that event
event_names = [single_event_name]
else:
event_names = self.events.keys()
for event_name in event_names:
event = self.events[event_name]
if self.event_type == 'SE' or self.event_type == 'RI':
gene = Gene.se_event_to_gene(event.up_part_len,
event.len,
event.dn_part_len,
event.chrom,
label=event.label)
elif self.event_type == 'TandemUTR':
gene = Gene.tandem_utr_event_to_gene(event.core_len,
event.ext_len,
event.chrom,
label=event.label)
elif (self.event_type == 'AFE' or self.event_type == 'ALE'):
gene = Gene.afe_ale_event_to_gene(event.proximal_exons,
event.distal_exons,
self.event_type,
event.chrom,
label=event.label,
read_len=read_len,
overhang_len=overhang_len)
else:
raise Exception, "Unsupported event type: %s" % (
self.event_type)
events_to_genes[event_name] = gene
t2 = time.time()
print "Parsing of events to genes took %.2f seconds." % (t2 - t1)
return events_to_genes
def loaded_events_to_genes(self, single_event_name=None,
read_len=None, overhang_len=None):
"""
Parse the loaded set of events into gene structures. Map events to genes.
"""
if len(self.events) == 0:
raise Exception, "Must load events first before they can be converted to genes."
events_to_genes = {}
t1 = time.time()
if single_event_name:
# If given an event name, only parse that event
event_names = [single_event_name]
else:
event_names = self.events.keys()
for event_name in event_names:
event = self.events[event_name]
if self.event_type == 'SE' or self.event_type == 'RI':
gene = Gene.se_event_to_gene(event.up_part_len, event.len, event.dn_part_len,
event.chrom,
label=event.label)
elif self.event_type == 'TandemUTR':
gene = Gene.tandem_utr_event_to_gene(event.core_len, event.ext_len,
event.chrom,
label=event.label)
elif (self.event_type == 'AFE' or self.event_type == 'ALE'):
gene = Gene.afe_ale_event_to_gene(event.proximal_exons, event.distal_exons,
self.event_type, event.chrom,
label=event.label, read_len=read_len,
overhang_len=overhang_len)
else:
raise Exception, "Unsupported event type: %s" %(self.event_type)
events_to_genes[event_name] = gene
t2 = time.time()
print "Parsing of events to genes took %.2f seconds." %(t2 - t1)
return events_to_genes
