def Worker_BlastScores(cmd_queue, seqsInfo, fileInfo, nProcesses, nToDo):
while True:
try:
i, args = cmd_queue.get(True, 1)
nDone = i - nProcesses + 1
if nDone >= 0 and divmod(nDone, 10 if nToDo <= 200 else 100 if nToDo <= 2000 else 1000)[1] == 0:
util.PrintTime("Done %d of %d" % (nDone, nToDo))
B = BlastFileProcessor.GetBLAST6Scores(seqsInfo, fileInfo, *args, qExcludeSelfHits = False)
matrices.DumpMatrix("Bit", B, fileInfo, args[0], args[1])
except Queue.Empty:
return
def Worker_BlastScores(cmd_queue, seqsInfo, fileInfo, nProcesses, nToDo):
while True:
try:
i, args = cmd_queue.get(True, 1)
nDone = i - nProcesses + 1
if nDone >= 0 and divmod(nDone, 10 if nToDo <= 200 else 100 if nToDo <= 2000 else 1000)[1] == 0:
util.PrintTime("Done %d of %d" % (nDone, nToDo))
B = BlastFileProcessor.GetBLAST6Scores(seqsInfo, fileInfo, *args, qExcludeSelfHits = False)
with open(fileInfo.workingDir + "Bit%d_%d.pic" % args, 'wb') as outfile:
pic.dump(B, outfile, protocol = util.picProtocol)
except Queue.Empty:
return
def Worker_OGMatrices_ReadBLASTAndUpdateDistances(cmd_queue, worker_status_queue, iWorker, ogMatrices, nGenes, seqsInfo, blastDir_list, ogsPerSpecies, qDoubleBlast):
speciesToUse = seqsInfo.speciesToUse
with np.errstate(divide='ignore'):
while True:
try:
iiSp, sp1, nSeqs_sp1 = cmd_queue.get(True, 1)
worker_status_queue.put(("start", iWorker, iiSp))
Bs = [BlastFileProcessor.GetBLAST6Scores(seqsInfo, blastDir_list, sp1, sp2, qExcludeSelfHits = False, qDoubleBlast=qDoubleBlast) for sp2 in speciesToUse]
mins = np.ones((nSeqs_sp1, 1), dtype=np.float64)*9e99
maxes = np.zeros((nSeqs_sp1, 1), dtype=np.float64)
for B in Bs:
m0, m1 = lil_minmax(B)
mins = np.minimum(mins, m0)
maxes = np.maximum(maxes, m1)
maxes_inv = 1./maxes
for jjSp, B in enumerate(Bs):
for og, m in zip(ogsPerSpecies, ogMatrices):
for gi, i in og[iiSp]:
for gj, j in og[jjSp]:
m[i][j] = 0.5*max(B[gi.iSeq, gj.iSeq], mins[gi.iSeq]) * maxes_inv[gi.iSeq]
worker_status_queue.put(("finish", iWorker, iiSp))
except Queue.Empty:
worker_status_queue.put(("empty", iWorker, None))
return