/usr/lib/python2.7/dist-packages/cogent/db/ensembl/species.py is in python-cogent 1.9-9.
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from cogent.db.ensembl.util import CaseInsensitiveString
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Gavin Huttley", "Jason Merkin"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Gavin Huttley"
__email__ = "Gavin.Huttley@anu.edu.au"
__status__ = "alpha"
_species_common_map = [['Acyrthosiphon pisum', 'A.pisum'],
['Aedes aegypti', 'A.aegypti'],
['Anolis carolinensis', 'Anole lizard'],
['Anopheles gambiae', 'A.gambiae'],
['Apis mellifera', 'Honeybee'],
['Arabidopsis lyrata', 'A.lyrata'],
['Arabidopsis thaliana', 'A.thaliana'],
['Aspergillus clavatus', 'A.clavatus'],
['Aspergillus flavus', 'A.flavus'],
['Aspergillus fumigatus', 'A.fumigatus'],
['Aspergillus fumigatusa1163', 'A.fumigatusa1163'],
['Aspergillus nidulans', 'A.nidulans'],
['Aspergillus niger', 'A.niger'],
['Aspergillus oryzae', 'A.oryzae'],
['Aspergillus terreus', 'A.terreus'],
['Bacillus collection', 'Bacillus'],
['Borrelia collection', 'Borrelia'],
['Bos taurus', 'Cow'],
['Brachypodium distachyon', 'B.distachyon'],
['Buchnera collection', 'Buchnera'],
['Caenorhabditis brenneri', 'C.brenneri'],
['Caenorhabditis briggsae', 'C.briggsae'],
['Caenorhabditis elegans', 'C.elegans'],
['Caenorhabditis japonica', 'C.japonica'],
['Caenorhabditis remanei', 'C.remanei'],
['Callithrix jacchus', 'Marmoset'],
['Canis familiaris', 'Dog'],
['Cavia porcellus', 'Guinea Pig'],
['Choloepus hoffmanni', 'Sloth'],
['Ciona intestinalis', 'C.intestinalis'],
['Ciona savignyi', 'C.savignyi'],
['Culex quinquefasciatus', 'C.quinquefasciatus'],
['Danio rerio', 'Zebrafish'],
['Dasypus novemcinctus', 'Armadillo'],
['Dictyostelium discoideum', 'D.discoideum'],
['Dipodomys ordii', 'Kangaroo rat'],
['Drosophila ananassae', 'D.ananassae'],
['Drosophila erecta', 'D.erecta'],
['Drosophila grimshawi', 'D.grimshawi'],
['Drosophila melanogaster', 'D.melanogaster'],
['Drosophila mojavensis', 'D.mojavensis'],
['Drosophila persimilis', 'D.persimilis'],
['Drosophila pseudoobscura', 'D.pseudoobscura'],
['Drosophila sechellia', 'D.sechellia'],
['Drosophila simulans', 'D.simulans'],
['Drosophila virilis', 'D.virilis'],
['Drosophila willistoni', 'D.willistoni'],
['Drosophila yakuba', 'D.yakuba'],
['Echinops telfairi', 'Tenrec'],
['Equus caballus', 'Horse'],
['Erinaceus europaeus', 'Hedgehog'],
['Escherichia shigella', 'E.shigella'],
['Felis catus', 'Cat'],
['Gallus gallus', 'Chicken'],
['Gasterosteus aculeatus', 'Stickleback'],
['Gorilla gorilla', 'Gorilla'],
['Homo sapiens', 'Human'],
['Ictidomys tridecemlineatus', 'Squirrel'],
['Ixodes scapularis', 'I.scapularis'],
['Loxodonta africana', 'Elephant'],
['Macaca mulatta', 'Macaque'],
['Macropus eugenii', 'Wallaby'],
['Microcebus murinus', 'Mouse lemur'],
['Monodelphis domestica', 'Opossum'],
['Mus musculus', 'Mouse'],
['Mycobacterium collection', 'Mycobacterium'],
['Myotis lucifugus', 'Microbat'],
['Neisseria collection', 'Neisseria'],
['Nematostella vectensis', 'N.vectensis'],
['Neosartorya fischeri', 'N.fischeri'],
['Neurospora crassa', 'N.crassa'],
['Ochotona princeps', 'Pika'],
['Ornithorhynchus anatinus', 'Platypus'],
['Oryctolagus cuniculus', 'Rabbit'],
['Oryza indica', 'O.indica'],
['Oryza sativa', 'O.sativa'],
['Oryzias latipes', 'Medaka'],
['Otolemur garnettii', 'Bushbaby'],
['Pan troglodytes', 'Chimp'],
['Pediculus humanus', 'P.humanus'],
['Petromyzon marinus', 'Lamprey'],
['Phaeodactylum tricornutum', 'P.tricornutum'],
['Physcomitrella patens', 'P.patens'],
['Phytophthora infestans', 'P.infestans'],
['Phytophthora ramorum', 'P.ramorum'],
['Phytophthora sojae', 'P.sojae'],
['Plasmodium berghei', 'P.berghei'],
['Plasmodium chabaudi', 'P.chabaudi'],
['Plasmodium falciparum', 'P.falciparum'],
['Plasmodium knowlesi', 'P.knowlesi'],
['Plasmodium vivax', 'P.vivax'],
['Pongo abelii', 'Orangutan'],
['Populus trichocarpa', 'P.trichocarpa'],
['Pristionchus pacificus', 'P.pacificus'],
['Procavia capensis', 'Rock hyrax'],
['Pteropus vampyrus', 'Flying fox'],
['Puccinia graministritici', 'P.graministritici'],
['Pyrococcus collection', 'Pyrococcus'],
['Rattus norvegicus', 'Rat'],
['Saccharomyces cerevisiae', 'S.cerevisiae'],
['Schistosoma mansoni', 'S.mansoni'],
['Schizosaccharomyces pombe', 'S.pombe'],
['Sorex araneus', 'Shrew'],
['Sorghum bicolor', 'S.bicolor'],
['Staphylococcus collection', 'Staphylococcus'],
['Streptococcus collection', 'Streptococcus'],
['Strongylocentrotus purpuratus', 'S.purpuratus'],
['Sus scrofa', 'Pig'],
['Taeniopygia guttata', 'Zebra finch'],
['Takifugu rubripes', 'Fugu'],
['Tarsius syrichta', 'Tarsier'],
['Tetraodon nigroviridis', 'Tetraodon'],
['Thalassiosira pseudonana', 'T.pseudonana'],
['Trichoplax adhaerens', 'T.adhaerens'],
['Tupaia belangeri', 'Tree Shrew'],
['Tursiops truncatus', 'Bottlenose dolphin'],
['Vicugna pacos', 'Alpaca'],
['Vitis vinifera', 'V.vinifera'],
['Wolbachia collection', 'Wolbachia'],
['Xenopus tropicalis', 'Xenopus'],
['Zea mays', 'Z.mays']]
class SpeciesNameMap(dict):
"""mapping between common names and latin names"""
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 __str__(self):
rows = []
for common in self._common_species:
species = self._common_species[common]
ensembl = self._species_ensembl[species]
rows += [[common, species, ensembl]]
return str(Table(['Common Name', 'Species Name', 'Ensembl Db Prefix'],
rows=rows, space=2).sorted())
def __repr__(self):
return 'Available species: %s' % ("'"+\
"'; '".join(self._common_species.keys())+"'")
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)
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 getSpeciesNames(self):
"""returns the list of species names"""
names = self._species_common.keys()
names.sort()
return [str(n) for n in names]
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 getComparaName(self, name):
"""returns string matching a compara instance attribute name for a
species"""
name = self.getCommonName(name)
if '.' in name:
name = name.replace('.', '')
else:
name = name.title()
name = name.split()
return ''.join(name)
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 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
Species = SpeciesNameMap()
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