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 testTaxonomyEntityPolymerReadCache(self):
"""Test case - evaluate taxonomy - from full cache"""
try:
taxIdList = [562, 9606, 3701]
for taxId in taxIdList:
tU = TaxonomyUtils(taxDirPath=self.__workPath)
tL = tU.getLineage(taxId)
logger.info("Taxonomy lineage for %d %r", taxId, tL)
#
#
epe = EntityPolymerExtractor(
self.__cfgOb,
saveCachePath=self.__fullEntitySaveCachePath,
useCache=True,
saveCacheKwargs=self.__fullCacheKwargs)
logger.info("Cache entry count %d", epe.getEntryCount())
logger.info(
"Reference sequences per ref db %r",
dict(sorted(epe.countRefSeqAccessionDbType().items())))
rD = epe.countRefSeqAccessionByTaxon(dbNameList=["UNP"])
logger.info("Unique taxons %d", len(list(rD.keys())))
#
numT = 0
for tId, aL in rD.items():
tL = tU.getLineage(tId)
if taxId in tL:
tc = len(set(aL))
logger.info("Matched %5d %s (%r)", tc,
tU.getScientificName(tId), tId)
numT += tc
logger.info("Total matched accessions %d ", numT)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()