def detect_fusions(data): data = to_single_data(data) # support the old style of fusion mode calling if dd.get_fusion_mode(data, False): data = dd.set_fusion_caller(data, ["oncofuse", "pizzly"]) logger.warning( "``fusion_mode`` is deprecated in favor of turning on " "callers with ``fusion_caller``. It will run pizzly and " "oncofuse for now, but will eventually have support " "dropped.") fusion_caller = dd.get_fusion_caller(data, []) if "oncofuse" in fusion_caller: oncofuse_file = oncofuse.run(data) if oncofuse_file: data = dd.set_oncofuse_file(data, oncofuse_file) if "pizzly" in fusion_caller: pizzly_dir = pizzly.run_pizzly(data) if pizzly_dir: data = dd.set_pizzly_dir(data, pizzly_dir) data["fusion"] = { "fasta": os.path.join(pizzly_dir, "%s.fusions.fasta" % dd.get_sample_name(data)), "json": os.path.join(pizzly_dir, "%s.json" % dd.get_sample_name(data)) } if "ericscript" in fusion_caller: ericscript_dir = ericscript.run(data) return [[data]]
def detect_fusions(data): if dd.get_fusion_mode(data, False): oncofuse_file = oncofuse.run(data) if oncofuse_file: data = dd.set_oncofuse_file(data, oncofuse_file) pizzly_dir = pizzly.run_pizzly(data) if pizzly_dir: data = dd.set_pizzly_dir(data, pizzly_dir) return [[data]]
def detect_fusions(data): # support the old style of fusion mode calling if dd.get_fusion_mode(data, False): data = dd.set_fusion_caller(data, ["oncofuse", "pizzly"]) logger.warning("``fusion_mode`` is deprecated in favor of turning on " "callers with ``fusion_caller``. It will run pizzly and " "oncofuse for now, but will eventually have support " "dropped.") if "oncofuse" in dd.get_fusion_caller(data, []): oncofuse_file = oncofuse.run(data) if oncofuse_file: data = dd.set_oncofuse_file(data, oncofuse_file) if "pizzly" in dd.get_fusion_caller(data, []): pizzly_dir = pizzly.run_pizzly(data) if pizzly_dir: data = dd.set_pizzly_dir(data, pizzly_dir) return [[data]]
def detect_fusions(data): data = to_single_data(data) # support the old style of fusion mode calling if dd.get_fusion_mode(data, False): data = dd.set_fusion_caller(data, ["oncofuse", "pizzly"]) logger.warning("``fusion_mode`` is deprecated in favor of turning on " "callers with ``fusion_caller``. It will run pizzly and " "oncofuse for now, but will eventually have support " "dropped.") fusion_caller = dd.get_fusion_caller(data, []) if "oncofuse" in fusion_caller: oncofuse_file = oncofuse.run(data) if oncofuse_file: data = dd.set_oncofuse_file(data, oncofuse_file) if "pizzly" in fusion_caller: pizzly_dir = pizzly.run_pizzly(data) if pizzly_dir: data = dd.set_pizzly_dir(data, pizzly_dir) data["fusion"] = {"fasta": os.path.join(pizzly_dir, "%s.fusions.fasta" % dd.get_sample_name(data)), "json": os.path.join(pizzly_dir, "%s.json" % dd.get_sample_name(data))} if "ericscript" in fusion_caller: ericscript_dir = ericscript.run(data) return [[data]]