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:raises: RuntimeError
""""""
#for path in self.path.values():
# if not os.path.exists(path):
# raise RuntimeError(""File '{}' is missing"".format(path))
for tool in ('cd-hit', 'prank', 'hmmbuild', 'hmmpress', 'hmmscan', 'phmmer', 'mafft', 'meme'):
if not self.pathfinder.exists(tool):
raise RuntimeError(""Dependency {} is missing"".format(tool))"
4405,"def generate_non_rabs(self):
"""""" Shrink the non-Rab DB size by reducing sequence redundancy.
""""""
logging.info('Building non-Rab DB')
run_cmd([self.pathfinder['cd-hit'], '-i', self.path['non_rab_db'], '-o', self.output['non_rab_db'],
'-d', '100', '-c', str(config['param']['non_rab_db_identity_threshold']), '-g', '1', '-T', self.cpu])
os.remove(self.output['non_rab_db'] + '.clstr')"
4406,"def parse_duration(duration):
""""""Attepmts to parse an ISO8601 formatted ``duration``.
Returns a ``datetime.timedelta`` object.
""""""
duration = str(duration).upper().strip()
elements = ELEMENTS.copy()
for pattern in (SIMPLE_DURATION, COMBINED_DURATION):
if pattern.match(duration):
found = pattern.match(duration).groupdict()
del found['time']
elements.update(dict((k, int(v or 0))
for k, v
in found.items()))
return datetime.timedelta(days=(elements['days'] +
_months_to_days(elements['months']) +
_years_to_days(elements['years'])),
hours=elements['hours'],
minutes=elements['minutes'],
seconds=elements['seconds'])
return ParseError()"
4407,"def skin_details(skin_id, lang=""en""):
""""""This resource returns details about a single skin.
:param skin_id: The skin to query for.
:param lang: The language to display the texts in.
The response is an object with at least the following properties. Note that
the availability of some properties depends on the type of item the skin
applies to.
skin_id (number):
The skin id.
name (string):
The name of the skin.
type (string):
The type of item the skin applies to. One of ``Armor``, ``Back`` or
``Weapon``.
flags (list):
Skin flags. Currently known skin flags are ``ShowInWardrobe``,
``HideIfLocked`` and ``NoCost``.
restrictions (list):
Race restrictions: ``Asura``, ``Charr``, ``Human``, ``Norn`` and
``Sylvari``.
icon_file_id (string):
The icon file id to be used with the render service.
icon_file_signature (string):
The icon file signature to be used with the render service.
""""""
params = {""skin_id"": skin_id, ""lang"": lang}
cache_name = ""skin_details.%(skin_id)s.%(lang)s.json"" % params
return get_cached(""skin_details.json"", cache_name, params=params)"
4408,"def bubble_to_dot(bblfile:str, dotfile:str=None, render:bool=False,
oriented:bool=False):
""""""Write in dotfile a graph equivalent to those depicted in bubble file""""""
tree = BubbleTree.from_bubble_file(bblfile, oriented=bool(oriented))
return tree_to_dot(tree, dotfile, render=render)"
4409,"def bubble_to_gexf(bblfile:str, gexffile:str=None, oriented:bool=False):
""""""Write in bblfile a graph equivalent to those depicted in bubble file""""""
tree = BubbleTree.from_bubble_file(bblfile, oriented=bool(oriented))
gexf_converter.tree_to_file(tree, gexffile)
return gexffile"
4410,"def bubble_to_js(bblfile:str, jsdir:str=None, oriented:bool=False, **style):
""""""Write in jsdir a graph equivalent to those depicted in bubble file""""""
js_converter.bubble_to_dir(bblfile, jsdir, oriented=bool(oriented), **style)
return jsdir"
4411,"def tree_to_dot(tree:BubbleTree, dotfile:str=None, render:bool=False):
""""""Write in dotfile a graph equivalent to those depicted in bubble file
See http://graphviz.readthedocs.io/en/latest/examples.html#cluster-py