#statsShuffles = RunningStats()
statsShuffles = OfflineStats()
recordsCount = 0
warningsCount = 0
rl = RateLimit(30)
total = countSpeciesCDS(taxId)
for protId in SpeciesCDSSource(taxId):
cds = CDSHelper(taxId, protId)
statsShuffles.push(
cds.dropShuffledSeqs(lastItemToKeep=args.keep_first_n_shuffles))
recordsCount += 1
if (rl()):
print("processed %d records (%.2g%%)" %
(recordsCount, float(recordsCount) / total * 100))
# DEBUG ONLY # DEBUG ONLY # DEBUG ONLY # DEBUG ONLY # DEBUG ONLY # DEBUG ONLY #
#if( recordsCount > 20 ):
# break
# DEBUG ONLY # DEBUG ONLY # DEBUG ONLY # DEBUG ONLY # DEBUG ONLY # DEBUG ONLY #
print(statsShuffles.count())
print("%.3g %.3g +-%.3g %.3g" % (statsShuffles.min(), statsShuffles.mean(), 2 *
statsShuffles.stdev(), statsShuffles.max()))
(taxId, getSpeciesName(taxId)))
print("Nothing left to do...")
sys.exit(0)
print("Species %d (%s) has %d proteins stored." %
(taxId, getSpeciesName(taxId), countSpeciesCDS(taxId)))
print("Will delete it in 10 seconds...")
sleep(10)
count = 0
for protId in SpeciesCDSSource(taxId):
print(protId)
cds = CDSHelper(taxId, protId)
try:
cds.dropShuffledSeqs()
except Exception as e:
print(e)
try:
cds.dropNativeSeq()
except Exception as e:
print(e)
cds.dropRecord()
count += 1
if (rl()):
print("Done processing %d records" % count)