def case_insensitive_keys(matcher_dict):
updated_dict = {MAP_SOURCES: matcher_dict[MAP_SOURCES],
MAP_GENE_ID: matcher_dict[MAP_GENE_ID],
MAP_LOCUS: matcher_dict[MAP_LOCUS],
MAP_SYNONYMS: defaultdict(list),
MAP_SYMBOL: defaultdict(list),
MAP_NOMENCLATURE: defaultdict(list)}
for key, value in matcher_dict[MAP_SYMBOL].items():
# ensure string, we are using string methods (upper, lower)
key = ensure_type(str(key), str)
updated_dict[MAP_SYMBOL][key] = value
updated_dict[MAP_SYMBOL][key.upper()] = value
updated_dict[MAP_SYMBOL][key.lower()] = value
for key, value in matcher_dict[MAP_SYNONYMS].items():
key = ensure_type(str(key), str)
updated_dict[MAP_SYNONYMS][key] = value
updated_dict[MAP_SYNONYMS][key.upper()] = value
updated_dict[MAP_SYNONYMS][key.lower()] = value
for key, value in matcher_dict[MAP_NOMENCLATURE].items():
key = ensure_type(str(key), str)
updated_dict[MAP_NOMENCLATURE][key] = value
updated_dict[MAP_NOMENCLATURE][key.upper()] = value
updated_dict[MAP_NOMENCLATURE][key.lower()] = value
return updated_dict
def __init__(self, tax_id, **kwargs):
self._organism = ensure_type(tax_id, str) # type: str
self._genes = [] # type: (List[str])
self._case_insensitive = kwargs.get("case_insensitive", False)
self._matcher = self.load_matcher_file(DOMAIN,
MATCHER_FILENAME.format(tax_id))
def __init__(self, tax_id, **kwargs):
""" Gene name matching interface
:param tax_id: Taxonomy if (NCBI taxonomy database)
:type tax_id: str
"""
self._organism = ensure_type(tax_id, str) # type: str
self._genes = [] # type: (List[Union[str, Gene]])
self._case_insensitive = kwargs.get("case_insensitive", False)
self._matcher = self.load_matcher_file(DOMAIN,
MATCHER_FILENAME.format(tax_id))
def update(self, sets):
# type: (List[GeneSet]) -> None
for g_set in sets:
self.add(ensure_type(g_set, GeneSet))
def __init__(self, sets=None):
# type: (List[GeneSet]) -> None
super().__init__()
if sets:
self.update(ensure_type(sets, list))
def organism(self, tax_id):
self._organism = ensure_type(tax_id, str)
self._matcher = self.load_matcher_file(DOMAIN, MATCHER_FILENAME.format(tax_id))
def __init__(self, tax_id):
self._organism = ensure_type(tax_id, str) # type: str
self._genes = [] # type: (List[str])
self._matcher = self.load_matcher_file(DOMAIN,
MATCHER_FILENAME.format(tax_id))
