def blat_pbsearch(fafile, file2bit, gfspath, gfcpath, threadnum, pblength, setpsize, dtm=10, minIdentity=75):
fa = loadfa.loadfa(fafile)
fa = fa.replace('n', '')
fa = fa.replace('N', '')
windlen = 1000000 # for real
# windlen = 10000 #for test
seqlen = len(fa)
sptime = int(seqlen/windlen)
pars = list()
pt = 0
chp = int(threadnum/6 - 1/6) + 1
for por in range(chp):
blatport = por+10010
t = threading.Thread(target=blat.start_gfServer, kwargs={'file2bit':file2bit, 'gfspath':gfspath, 'stepsize':setpsize, 'blatport':blatport})
t.daemon = True
t.start()
print("starting gfServer ... ")
time.sleep(100)
for sc in range(sptime+1):
nowstart = sc * windlen
nowend = nowstart + windlen + 50
if nowend > seqlen:
nowend = seqlen-1
nowseq = fa[nowstart:nowend]
blatport = 10010 + random.randint(0, chp-1)
pt = 1 + pt
par = dict()
print (nowstart,nowend,blatport)
par['sequence'] = nowseq
par['blatport'] = blatport
par['gfcpath'] = gfcpath
par['pblength'] = pblength
par['file2bit'] = file2bit
par['dtm'] = dtm
par['minIdentity'] = minIdentity
pars.append(par)
par2 = dict()
blatport = 10010
nowstart = windlen * sptime
nowend = seqlen-1
nowseq = fa[nowstart:nowend]
par2['sequence'] = nowseq
par2['blatport'] = blatport
par2['gfcpath'] = gfcpath
par2['pblength'] = pblength
par2['file2bit'] = file2bit
par2['dtm'] = dtm
par2['minIdentity'] = minIdentity
pars.append(par2)
pool = Pool(threadnum)
res = pool.map(blat_getseqlen, pars)
probe = dict()
for i in res:
for j in i:
if j in probe:
probe[j] = +1
else:
probe[j] = 1
blat.stop_gfServer()
# probecount = Counter
#
# for probeseq in probe:
#
# probecount[probeseq] += 1
probelist = list()
for probeseq in probe:
if probe[probeseq] == 1:
probelist.append(probeseq)
return probelist
def exonerate_pbsearch(fafile, esifile, espath, ep, threadnum, pblength, setpsize, dtm=10, minIdentity=75,
exonerateport=10005):
fa = loadfa.loadfa(fafile)
fa = fa.replace('n', '')
fa = fa.replace('N', '')
seqlen = len(fa)
windlen = 10000
sptime = int(seqlen/windlen)+1
pars = list()
#start exonerate server
# exonerate.start_exonerate_server(espath=espath, esifile=esifile, threadnum=24, exonerateport=exonerateport)
time.sleep(10)
for sc in range(sptime):
nowstart = sc * windlen
nowend = nowstart + windlen + 50
if nowend > seqlen:
nowend = seqlen-1
nowseq = fa[nowstart:nowend]
# print(nowseq)
par = dict()
par['sequence'] = nowseq
par['exonerateport'] = exonerateport
par['ep'] = ep
par['minIdentity'] = minIdentity
par['pblength'] = pblength
pars.append(par)
pool = Pool(threadnum)
res = pool.map(exonerate_getseqlen, pars)
probe = dict()
for i in res:
for j in i:
if j in probe:
probe[j] = +1
else:
probe[j] = 1
exonerate.stop_exonerate_server()
probelist = list()
print(probe)
for probeseq in probe:
if probe[probeseq] == 1:
probelist.append(probeseq)
return probelist
