def testAccessEntityPolymerReadCache(self): """Test case - access cached entity polymer info from test cache""" try: epe = EntityPolymerExtractor(self.__cfgOb, exdbDirPath=self.__exdbCacheDirPath, useCache=False, cacheKwargs=self.__cacheKwargs) logger.info("Cache entry count %d", epe.getEntryCount()) cD = epe.countRefSeqAccessions("UNP") self.assertGreaterEqual(len(cD), 2) logger.info("UNP reference sequences per entity %r", dict(sorted(cD.items()))) logger.info("Reference sequences per entity %r", dict(sorted(epe.countRefSeqAccessionAny().items()))) logger.info("Reference sequences per ref db %r", dict(sorted(epe.countRefSeqAccessionDbType().items()))) # ok = epe.checkRefSeqAlignRange("UNP") self.assertTrue(ok) unpL = epe.getRefSeqAccessions("UNP") logger.info("Unique UNP reference sequences %d", len(unpL)) self.assertTrue(ok) tD = epe.getUniqueTaxons() logger.info("Unique taxons %d", len(tD)) tD = epe.countRefSeqAccessionByTaxon("UNP") logger.info("Unique taxons %d", len(tD)) # except Exception as e: logger.exception("Failing with %s", str(e)) self.fail()
def testAccessEntityPolymerFeatures(self): """Test case - access cached entity polymer info from full cache""" try: epe = EntityPolymerExtractor( self.__cfgOb, saveCachePath=self.__fullEntitySaveCachePath, useCache=True, saveCacheKwargs=self.__fullCacheKwargs) eCount = epe.getEntryCount() logger.info("Entry count %d", eCount) self.assertGreaterEqual(eCount, self.__entryLimitFull) # unpL = epe.getRefSeqAccessions("UNP") logger.info("Ref seq count %d", len(unpL)) self.assertGreaterEqual(len(unpL), 1) # testOp = False if testOp: for entryId in ["1CP9"]: for entityId in ["1", "2"]: uL = epe.getEntityRefSeqAccessions( "UNP", entryId, entityId) logger.debug("UNP for %s %s %r", entryId, entityId, uL) # except Exception as e: logger.exception("Failing with %s", str(e)) self.fail()
def __getReferenceAssignments(self, refDbName, **kwargs): """Get all accessions assigned to input reference sequence database""" rL = [] exdbDirPath = kwargs.get("exdbDirPath", None) cacheKwargs = kwargs.get("cacheKwargs", None) useCache = kwargs.get("useCache", True) entryLimit = kwargs.get("entryLimit", None) try: epe = EntityPolymerExtractor(self.__cfgOb, exdbDirPath=exdbDirPath, useCache=useCache, cacheKwargs=cacheKwargs, entryLimit=entryLimit) eCount = epe.getEntryCount() rL = epe.getRefSeqAccessions(refDbName) logger.info( "Reading polymer entity cache with repository entry count %d ref accession length %d ", eCount, len(rL)) # except Exception as e: logger.exception("Failing with %s", str(e)) return rL
def testAccessEntityPolymerFeatures(self): """Test case - access cached entity polymer info from test cache""" try: epe = EntityPolymerExtractor(self.__cfgOb, exdbDirPath=self.__exdbCacheDirPath, useCache=False, cacheKwargs=self.__cacheKwargs) eCount = epe.getEntryCount() logger.info("Entry count %d", eCount) self.assertGreaterEqual(eCount, self.__entryLimitTest) # unpL = epe.getRefSeqAccessions("UNP") logger.info("Ref seq count %d", len(unpL)) self.assertGreaterEqual(len(unpL), 1) # for entryId in ["3RER"]: for entityId in ["1"]: uL = epe.getEntityRefSeqAccessions("UNP", entryId, entityId) logger.info("UNP for %s %s %r", entryId, entityId, uL) # except Exception as e: logger.exception("Failing with %s", str(e)) self.fail()