from cogent.util.table import Table from cogent.db.ensembl.util import CaseInsensitiveString __author__ = "Gavin Huttley" __copyright__ = "Copyright 2007-2012, The Cogent Project" __credits__ = ["Gavin Huttley", "Jason Merkin"] __license__ = "GPL" __version__ = "1.5.3" __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'], ['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 pygmaeus', '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'], ['Spermophilus tridecemlineatus', 'Ground Squirrel'], ['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): """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 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()