def importNewPairs(self,
pairs, # csv containing information about new pairs to process
paths # absolute paths to new genome fasta files referenced in pairs
):
print "Importing new pairs from: %s" % pairs
print "Import full contig file paths from: %s" % paths
# get an interface to the file
II = ImportInterface(self.dbFileName)
# import paths first
with open(paths, "r") as paths_fh:
II.importGenomes(paths_fh)
# import genomes next
with open(pairs, "r") as pairs_fh:
II.importPairs(pairs_fh)
def _updateHits(self, contigHeaders, resultQueue, hitCache):
II = ImportInterface(self.dbFileName,verbosity=-1)
tmp = []
while(True):
current = resultQueue.get(block=True, timeout=None)
#print "current capacity of resultQueue %d" % int(resultQueue.qsize())
if current == None:
#print ">> DBG Current is None"
II.importHits(contigHeaders, tmp)
break
else:
tmp.append(current)
#print ">> DBG Length of tmp is %d" % len(tmp)
if len(tmp) >= hitCache: # set size limit of queue
print ">> DBG " + datetime.datetime.fromtimestamp(time.time()).strftime('%Y-%m-%d %H:%M:%S') + " Length of tmp is %d :: current capacity of resultQueue %d" % (len(tmp), int(resultQueue.qsize()))
II.importHits(contigHeaders, tmp)
tmp = []
