def __init__(self, species_common=_species_common_map):
"""provides latin name:common name mappings"""
self._species_common = {}
self._common_species = {}
self._species_ensembl = {}
self._ensembl_species = {}
for species_name, common_name in species_common:
self.amendSpecies(CaseInsensitiveString(species_name),
CaseInsensitiveString(common_name))
def amendSpecies(self, species_name, common_name):
"""add a new species, and common name"""
species_name = CaseInsensitiveString(species_name)
common_name = CaseInsensitiveString(common_name)
assert "_" not in species_name,\
"'_' in species_name, not a Latin name?"
self._purge_species(species_name) # remove if existing
self._species_common[species_name] = common_name
self._common_species[common_name] = species_name
ensembl_name = species_name.lower().replace(" ", "_")
self._species_ensembl[species_name] = ensembl_name
self._ensembl_species[ensembl_name] = species_name
return
def amendSpecies(self, species_name, common_name):
"""add a new species, and common name"""
species_name = CaseInsensitiveString(species_name)
common_name = CaseInsensitiveString(common_name)
assert "_" not in species_name,\
"'_' in species_name, not a Latin name?"
self._purge_species(species_name) # remove if existing
self._species_common[species_name] = common_name
self._common_species[common_name] = species_name
ensembl_name = species_name.lower().replace(" ","_")
self._species_ensembl[species_name] = ensembl_name
self._ensembl_species[ensembl_name] = species_name
return
def _purge_species(self, species_name):
"""removes a species record"""
species_name = CaseInsensitiveString(species_name)
if not species_name in self._species_common:
return
common_name = self._species_common.pop(species_name)
ensembl_name = self._species_ensembl.pop(species_name)
self._ensembl_species.pop(ensembl_name)
self._common_species.pop(common_name)
def getEnsemblDbPrefix(self, name):
"""returns a string of the species name in the format used by
ensembl"""
name = CaseInsensitiveString(name)
if name in self._common_species:
name = self._common_species[name]
try:
species_name = self.getSpeciesName(name, level='raise')
except RuntimeError:
if name not in self._species_common:
raise RuntimeError("Unknown name %s" % name)
species_name = name
return str(species_name.lower().replace(" ", "_"))
def getCommonName(self, name):
"""returns the common name for the given name (which can be either a
species name or the ensembl version)"""
name = CaseInsensitiveString(name)
if name in self._ensembl_species:
name = self._ensembl_species[name]
if name in self._species_common:
common_name = self._species_common[name]
elif name in self._common_species:
common_name = name
else:
raise RuntimeError("Unknown species: %s" % name)
return str(common_name)
def getSpeciesName(self, name, level='ignore'):
"""returns the species name for the given common name"""
name = CaseInsensitiveString(name)
if name in self._species_common:
return str(name)
species_name = None
level = level.lower().strip()
name = name
for data in [self._common_species, self._ensembl_species]:
if name in data:
species_name = data[name]
if species_name is None:
msg = "Unknown common name: %s" % name
if level == 'raise':
raise RuntimeError(msg)
elif level == 'warn':
print "WARN: %s" % msg
return str(species_name)
def getCommonName(self, name, level='raise'):
"""returns the common name for the given name (which can be either a
species name or the ensembl version)"""
name = CaseInsensitiveString(name)
if name in self._ensembl_species:
name = self._ensembl_species[name]
if name in self._species_common:
common_name = self._species_common[name]
elif name in self._common_species:
common_name = name
else:
common_name = None
if common_name is None:
msg = "Unknown species name: %s" % name
if level == 'raise':
raise RuntimeError(msg)
elif level == 'warn':
print "WARN: %s" % msg
return str(common_name)