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In cases where the direct children of a gene feature have heterogenous
types, the `primary_mrna` function will only discard mRNA features. This
function, however, will discard all direct children of the gene that are
not the primary transcript, including non-transcript children. This is a
retty subtle distinction, and anecdotal experience suggests that cases in
which the distinction actually matters are extremely rare.
""""""
for entry in entrystream:
if not isinstance(entry, tag.Feature):
yield entry
continue
for parent in tag.select.features(entry, parenttype, traverse=True):
if parent.num_children == 0:
continue
transcripts = defaultdict(list)
for child in parent.children:
if child.type in type_terms:
transcripts[child.type].append(child)
if len(transcripts) == 0:
continue
ttypes = list(transcripts.keys())
ttype = _get_primary_type(ttypes, parent)
transcript_list = transcripts[ttype]
if ttype == 'mRNA':
_emplace_pmrna(transcript_list, parent, strict=True)
else:
_emplace_transcript(transcript_list, parent)
yield entry"
3777,"def parse_parent(docname):
"""""" Given a docname path, pick apart and return name of parent """"""
lineage = docname.split('/')
lineage_count = len(lineage)
if docname == 'index':
# This is the top of the Sphinx project
parent = None
elif lineage_count == 1:
# This is a non-index doc in root, e.g. about
parent = 'index'
elif lineage_count == 2 and lineage[-1] == 'index':
# This is blog/index, parent is the root
parent = 'index'
elif lineage_count == 2:
# This is blog/about
parent = lineage[0] + '/index'
elif lineage[-1] == 'index':
# This is blog/sub/index
parent = '/'.join(lineage[:-2]) + '/index'
else:
# This should be blog/sub/about
parent = '/'.join(lineage[:-1]) + '/index'
return parent"
3778,"def parents(self, resources):
"""""" Split the path in name and get parents """"""
if self.docname == 'index':
# The root has no parents
return []
parents = []
parent = resources.get(self.parent)
while parent is not None:
parents.append(parent)
parent = resources.get(parent.parent)
return parents"
3779,"def acquire(self, resources, prop_name):
"""""" Starting with self, walk until you find prop or None """"""
# Instance
custom_prop = getattr(self.props, prop_name, None)
if custom_prop:
return custom_prop
# Parents...can't use acquire as have to keep going on acquireds
for parent in self.parents(resources):
acquireds = parent.props.acquireds
if acquireds:
# First try in the per-type acquireds
rtype_acquireds = acquireds.get(self.rtype)
if rtype_acquireds:
prop_acquired = rtype_acquireds.get(prop_name)
if prop_acquired:
return prop_acquired
# Next in the ""all"" section of acquireds
all_acquireds = acquireds.get('all')
if all_acquireds:
prop_acquired = all_acquireds.get(prop_name)
if prop_acquired:
return prop_acquired
return"