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]]
