def register_task_handler(obj, handler_obj, default_handler=None):
"""Register a module function represented as string in
to a task handler.
:param obj: the object to which the handler is registered
:param handler_obj: the handler object to register
:param default_handler: the default handler to fall back on
:return: None
"""
if not handler_obj:
logging.warn("No handler object provided; skipping")
return
if not isinstance(handler_obj, IHandler):
raise ValueError, "handler object must implement the IHandler interface"
hdl = _load(handler_obj)
if not hdl:
return
if handler_obj.label() in obj._handlers:
old_hdl = obj._handlers[handler_obj.label()]
if fullclassname(old_hdl) == fullclassname(hdl):
logging.info("Handler object '{}' already registered in {}; skipping".format(fullclassname(hdl), obj))
return
else:
logging.warn("Trying to reset already registered '{}' which is not supported".format(handler_obj.label()))
return
else:
obj._handlers[handler_obj.label()] = hdl
def register_task_handler(obj, handler_obj, default_handler=None):
"""Register a module function represented as string in
to a task handler.
:param obj: the object to which the handler is registered
:param handler_obj: the handler object to register
:param default_handler: the default handler to fall back on
:return: None
"""
if not handler_obj:
logging.warn("No handler object provided; skipping")
return
if not isinstance(handler_obj, IHandler):
raise ValueError, "handler object must implement the IHandler interface"
hdl = _load(handler_obj)
if not hdl:
return
if handler_obj.label() in obj._handlers:
old_hdl = obj._handlers[handler_obj.label()]
if fullclassname(old_hdl) == fullclassname(hdl):
logging.info(
"Handler object '{}' already registered in {}; skipping".
format(fullclassname(hdl), obj))
return
else:
logging.warn(
"Trying to reset already registered '{}' which is not supported"
.format(handler_obj.label()))
return
else:
obj._handlers[handler_obj.label()] = hdl
def test_register_task_handler(self):
obj = MergeSamFiles()
obj._handlers = {}
target_handler = RatatoskHandler(label="target_generator_handler", mod="test.test_handler.local_target_generator")
self.assertEqual(obj._handlers, {})
register_task_handler(obj, target_handler)
self.assertEqual(fullclassname(obj._handlers['target_generator_handler']), "test.test_handler.local_target_generator")
def test_register_handler(self):
backend.__handlers__ = {}
target_handler = RatatoskHandler(
label="target_generator_handler",
mod="test.test_handler.local_target_generator")
self.assertEqual(backend.__handlers__, {})
register(target_handler)
self.assertEqual(
fullclassname(backend.__handlers__['target_generator_handler']),
"test.test_handler.local_target_generator")
def test_register_task_handler(self):
obj = MergeSamFiles()
obj._handlers = {}
target_handler = RatatoskHandler(
label="target_generator_handler",
mod="test.test_handler.local_target_generator")
self.assertEqual(obj._handlers, {})
register_task_handler(obj, target_handler)
self.assertEqual(
fullclassname(obj._handlers['target_generator_handler']),
"test.test_handler.local_target_generator")
def requires(self):
vcfcls = self.parent()[0]
indexcls = ratatosk.lib.variation.tabix.Tabix
return [
cls(target=source)
for cls, source in izip(self.parent(), self.source())
] + [
indexcls(target=rreplace(self.source()[0],
vcfcls().suffix,
indexcls().suffix, 1),
parent_task=fullclassname(vcfcls))
]
def requires(self):
"""Task requirements. In many cases this is a single source
whose name can be generated following the code below, and
therefore doesn't need reimplementation in the subclasses."""
bamcls = self.parent()[0]
indexcls = ratatosk.lib.tools.samtools.Index
return [bamcls(target=self.source()[0])] + [
CombineVariants(
target=os.path.join(self.outdir, "CombinedVariants.vcf"))
] + [
indexcls(target=rreplace(self.source()[0],
bamcls().sfx(),
indexcls().sfx(), 1),
parent_task=fullclassname(bamcls))
]
def requires(self):
"""Task requirements. In many cases this is a single source
whose name can be generated following the code below, and
therefore doesn't need reimplementation in the subclasses."""
bamcls = self.parent()[0]
indexcls = ratatosk.lib.tools.samtools.Index
return [
cls(target=source)
for cls, source in izip(self.parent(), self.source())
] + [
indexcls(target=rreplace(self.source()[0],
bamcls().sfx(),
indexcls().sfx(), 1),
parent_task=fullclassname(bamcls))
]
def requires(self):
cls = self.set_parent_task()
source = self._make_source_file_name()
# Ugly hack for 1 -> 2 dependency: works but should be dealt with otherwise
if str(fullclassname(cls)) in ["ratatosk.lib.utils.misc.ResyncMatesJobTask"]:
if re.search(self.read1_suffix, source):
self.is_read1 = True
fq1 = source
fq2 = rreplace(source, self.read1_suffix, self.read2_suffix, 1)
else:
self.is_read1 = False
fq1 = rreplace(source, self.read2_suffix, self.read1_suffix, 1)
fq2 = source
return cls(target=[fq1, fq2])
else:
return cls(target=source)
def requires(self):
cls = self.parent()[0]
source = self.source()[0]
# Ugly hack for 1 -> 2 dependency: works but should be dealt with otherwise
if str(fullclassname(cls)) in ["ratatosk.lib.utils.misc.ResyncMates"]:
rt = determine_read_type(source, self.read1_suffix, self.read2_suffix)
if rt == 1:
self.is_read1 = True
fq1 = source
fq2 = rreplace(source, self.read1_suffix, self.read2_suffix, 1)
elif rt == 2:
self.is_read1 = False
fq1 = rreplace(source, self.read2_suffix, self.read1_suffix, 1)
fq2 = source
retval = [cls(target=[fq1, fq2])]
else:
retval = [cls(target=source)]
if len(self.parent()) > 1:
retval += [cls(target=source) for cls, source in izip(self.parent()[1:], self.source()[1:])]
return retval
def requires(self):
"""Task requirements. In many cases this is a single source
whose name can be generated following the code below, and
therefore doesn't need reimplementation in the subclasses."""
bamcls = self.parent()[0]
indexcls = ratatosk.lib.tools.samtools.Index
return [bamcls(target=self.source()[0])] + [CombineVariants(target=os.path.join(self.outdir, "CombinedVariants.vcf"))] + [indexcls(target=rreplace(self.source()[0], bamcls().sfx(), indexcls().sfx(), 1), parent_task=fullclassname(bamcls))]
def test_register_handler(self):
backend.__handlers__ = {}
target_handler = RatatoskHandler(label="target_generator_handler", mod="test.test_handler.local_target_generator")
self.assertEqual(backend.__handlers__, {})
register(target_handler)
self.assertEqual(fullclassname(backend.__handlers__['target_generator_handler']), "test.test_handler.local_target_generator")
def requires(self):
"""Task requirements. In many cases this is a single source
whose name can be generated following the code below, and
therefore doesn't need reimplementation in the subclasses."""
bamcls = self.parent()[0]
indexcls = ratatosk.lib.tools.samtools.Index
return [cls(target=source) for cls, source in izip(self.parent(), self.source())] + [indexcls(target=rreplace(self.source()[0], bamcls().sfx(), indexcls().sfx(), 1), parent_task=fullclassname(bamcls))]
def requires(self):
cls = self.set_parent_task()
source = self._make_source_file_name()
return [cls(target=source), ratatosk.lib.tools.samtools.IndexBam(target=rreplace(source, self.source_suffix, ".bai", 1), parent_task=fullclassname(cls))]
def requires(self):
vcfcls = self.parent()[0]
indexcls = ratatosk.lib.variation.tabix.Tabix
return [cls(target=source) for cls, source in izip(self.parent(), self.source())] + [indexcls(target=rreplace(self.source()[0], vcfcls().suffix, indexcls().suffix, 1), parent_task=fullclassname(vcfcls))]
def requires(self):
zipcls = ratatosk.lib.variation.tabix.Bgzip
indexcls = ratatosk.lib.variation.tabix.Tabix
return [zipcls(target=self.source()[0]),
indexcls(target=rreplace(self.source()[0], zipcls().sfx(), indexcls().sfx(), 1),
parent_task=fullclassname(zipcls))]