def name_or_none(taxid): """Return organism name for ncbi taxid or None if not found. """ try: return taxonomy.name(taxid) except taxonomy.UnknownSpeciesIdentifier: return None
def initialize(self): if self.__initialized: # Already initialized return self.__initialized = True self.organisms = sorted( set([ name.split(".")[-2] for name in serverfiles.listfiles("NCBI_geneinfo") ] + gene.NCBIGeneInfo.common_taxids())) self.organismComboBox.addItems( [taxonomy.name(tax_id) for tax_id in self.organisms]) if self.taxid in self.organisms: self.organism_index = self.organisms.index(self.taxid) else: self.organism_index = 0 self.taxid = self.organisms[self.organism_index] self.altSourceCheck.setVisible(self.taxid == DICTY_TAXID) self.dictyExpressBox.setVisible(self.taxid == DICTY_TAXID) self.infoLabel.setText("No data on input\n") self.initfuture = None self.setBlocking(False) self.progressBarFinished(processEvents=None)
def initialize(self): if self.__initialized: # Already initialized return self.__initialized = True self.organisms = sorted( set([name.split(".")[-2] for name in serverfiles.listfiles("NCBI_geneinfo")] + gene.NCBIGeneInfo.common_taxids()) ) self.organismComboBox.addItems( [taxonomy.name(tax_id) for tax_id in self.organisms] ) if self.taxid in self.organisms: self.organism_index = self.organisms.index(self.taxid) else: self.organism_index = 0 self.taxid = self.organisms[self.organism_index] self.altSourceCheck.setVisible(self.taxid == DICTY_TAXID) self.dictyExpressBox.setVisible(self.taxid == DICTY_TAXID) self.infoLabel.setText("No data on input\n") self.initfuture = None self.setBlocking(False) self.progressBarFinished(processEvents=None)
def setUp(self): self.listfiles = [ fname for domain, fname in sf_local.listfiles("NCBI_geneinfo") ] self.taxonomy_IDs = sorted( set([name.split(".")[-2] for name in self.listfiles] + NCBIGeneInfo.common_taxids())) self.organisms = [(taxonomy.name(tax_id), tax_id) for tax_id in self.taxonomy_IDs]
force = False # force update taxids = ppi.STRING.common_taxids() desc = "STRING Protein interactions for {name} (Creative Commons Attribution 3.0 License)" #Sorry, STRING does not know an organism named 'Mycoplasma pneumoniae M129', ' Candida albicans'. #Note that the database only contains organisms with full sequenced and published genomes. exclude = ['272634', '5476'] taxids = [idtax for idtax in taxids if idtax not in exclude] for taxid in taxids: dbfilename = ppi.STRING.default_db_filename(taxid) basename = os.path.basename(dbfilename) TITLE = desc.format(name=taxonomy.name(taxid)) TAGS = ["protein interaction", "STRING"] VERSION = ppi.STRING.VERSION if not force and version_id in sf_server.info("PPI", basename)["tags"]: continue ppi.STRING.init_db(version, taxid, dbfilename=dbfilename, cache_dir=downloads) gzfile = gzip.GzipFile(os.path.join(temp_path, basename), "wb") shutil.copyfileobj(open(dbfilename, "rb"), gzfile) gzfile.close()
taxids = ppi.STRING.common_taxids() desc = "STRING Protein interactions for {name} (Creative Commons Attribution 3.0 License)" #Sorry, STRING does not know an organism named 'Mycoplasma pneumoniae M129', ' Candida albicans'. #Note that the database only contains organisms with full sequenced and published genomes. exclude = ['272634', '5476'] taxids = [idtax for idtax in taxids if idtax not in exclude] for taxid in taxids: dbfilename = ppi.STRING.default_db_filename(taxid) basename = os.path.basename(dbfilename) TITLE = desc.format(name=taxonomy.name(taxid)) TAGS = ["protein interaction", "STRING"] VERSION = ppi.STRING.VERSION if not force and version_id in sf_server.info("PPI", basename)["tags"]: continue ppi.STRING.init_db(version, taxid, dbfilename=dbfilename, cache_dir=downloads) gzfile = gzip.GzipFile(os.path.join(temp_path, basename), "wb") shutil.copyfileobj(open(dbfilename, "rb"), gzfile) gzfile.close() create_info_file(os.path.join(temp_path, basename), title=TITLE, tags=TAGS, version=VERSION, compression='gz', uncompressed=file_size_bytes(dbfilename), dbversion=version_id)
def setUp(self): self.common_ids = taxonomy.common_taxids() self.organisms = [(taxonomy.name(tax_id), tax_id) for tax_id in self.common_ids] self.taxon = taxonomy.Taxonomy()
def setUp(self): self.listfiles = [fname for domain, fname in sf_local.listfiles("NCBI_geneinfo")] self.taxonomy_IDs = sorted(set([name.split(".")[-2] for name in self.listfiles] + NCBIGeneInfo.common_taxids())) self.organisms = [(taxonomy.name(tax_id), tax_id) for tax_id in self.taxonomy_IDs]