def main():
args = check_options(get_options())
genomesize = int(os.path.getsize(args.genome)/1e6)
kmer = int(log(genomesize, 4)+1)
if kmer < 17:
kmer = 17
#jellyfish par
lowercount = 2
#jellyfish par
jfsize = '100M'
# splite sequence longer than 10M
spsize = 10000000
step = args.step
maxkmerscore = int(((args.length * args.homology / 100) - kmer) * args.ploidy/2 + 0.5 )
jfpool = Pool(args.threads)
# ?build kmerindex
jfkmerfile = os.path.join(args.saved,(os.path.basename(args.genome)+'_'+str(kmer)+'mer.jf'))
kmerbuild = True
if os.path.isfile(jfkmerfile):
if not args.docker:
print("find:", jfkmerfile)
kmmess = "Found kmerfile "+jfkmerfile+". Do you want rebuild it? Press Y or N to continue:"
print(kmmess)
while True:
char = getch()
if char.lower() in ("y", "n"):
print(char)
if char == 'y':
kmerbuild = True
elif char == 'n':
kmerbuild = False
break
# ?build bwa index
bwaindexfile = os.path.basename(args.genome)
bwatestindex = os.path.join(args.saved, bwaindexfile+'.sa')
bwaindex = os.path.join(args.saved, bwaindexfile)
bwabuild = True
if os.path.isfile(bwatestindex):
if not args.docker:
print('find:', bwatestindex)
bwamess = "Found bwa index file " + bwatestindex + ". Do you want rebuild it? Press Y or N to continue:"
print(bwamess)
while True:
char = getch()
if char.lower() in ("y", "n"):
print(char)
if char == 'y':
bwabuild = True
elif char == 'n':
bwabuild = False
break
print("genomesize:",genomesize, "kmer:",kmer, "jfkmerfile:",
jfkmerfile, "kmerbuild:", kmerbuild, "bwabuild:", bwabuild, "threads:", args.threads)
# Build Jellyfish index
if kmerbuild:
jfcount = jellyfish.jfcount(jfpath=args.jellyfish, mer=kmer, infile=args.genome, output=jfkmerfile,
threads=args.threads, lowercount=lowercount, size=jfsize)
if jfcount:
print("JellyFish Count finished ...")
else:
print("JellyFish Count Error!!!")
sys.exit(1)
else:
print("Use ", jfkmerfile)
# End build Jellyfish index
if bwabuild:
bwa.bwaindex(args.bwa, args.genome, args.saved)
print("bwa index build finished ...")
else:
print("Use", bwatestindex)
jffilteredprobe = list()
#####
if genomesize < 1000:
fastain = Fasta(args.input)
jffpbrunerlist = list()
for seqname in fastain.keys():
chrlen = len(fastain[seqname])
if chrlen < spsize:
start = 0
end = chrlen - 1
jffpbruner = jellyfish.JFfpbruner(jfpath=args.jellyfish, jfkmerfile=jfkmerfile, mer=kmer,
pyfasta=fastain, seqname=seqname, pblength=args.length,
maxkmerscore=maxkmerscore, start=start,
end=end, step=step)
jffpbrunerlist.append(jffpbruner)
else:
chrblock = int(chrlen/spsize) + 1
for i in range(chrblock):
start = i * spsize
end = start + spsize - 1
if end >= chrlen:
end = chrlen - 1
jffpbruner = jellyfish.JFfpbruner(jfpath=args.jellyfish, jfkmerfile=jfkmerfile, mer=kmer,
pyfasta=fastain, seqname=seqname, pblength=args.length,
maxkmerscore=maxkmerscore, start=start,
end=end, step=step)
jffpbrunerlist.append(jffpbruner)
jffinished = 0
print(len(jffpbrunerlist))
for curpblist in jfpool.imap_unordered(jellyfish.kmerfilterprobe, jffpbrunerlist):
jffilteredprobe.extend(curpblist)
jffinished += 1
print("Jellyfish filter: ",jffinished,'/',len(jffpbrunerlist), sep='')
jfpool.close()
print('Jellyfish filter finished!!')
else:
### split fa file when geome size greater than 1 Gb
print("genome size > 1G")
subFas = spgenome.spgenome(args.input, args.saved)
for subFafile in subFas:
print(subFafile)
fastain = Fasta(subFafile)
jffpbrunerlist = list()
for seqname in fastain.keys():
chrlen = len(fastain[seqname])
if chrlen < spsize:
start = 0
end = chrlen - 1
jffpbruner = jellyfish.JFfpbruner(jfpath=args.jellyfish, jfkmerfile=jfkmerfile, mer=kmer,
pyfasta=fastain, seqname=seqname, pblength=args.length,
maxkmerscore=maxkmerscore, start=start,
end=end, step=step)
jffpbrunerlist.append(jffpbruner)
else:
chrblock = int(chrlen / spsize) + 1
for i in range(chrblock):
start = i * spsize
end = start + spsize - 1
if end >= chrlen:
end = chrlen - 1
jffpbruner = jellyfish.JFfpbruner(jfpath=args.jellyfish, jfkmerfile=jfkmerfile, mer=kmer,
pyfasta=fastain, seqname=seqname, pblength=args.length,
maxkmerscore=maxkmerscore, start=start,
end=end, step=step)
jffpbrunerlist.append(jffpbruner)
jffinished = 0
print(len(jffpbrunerlist))
for curpblist in jfpool.imap_unordered(jellyfish.kmerfilterprobe, jffpbrunerlist):
jffilteredprobe.extend(curpblist)
jffinished += 1
print(subFafile + " Jellyfish filter: ", jffinished, '/', len(jffpbrunerlist), sep='')
jfpool.close()
print('Jellyfish filter finished!!')
tmppbfa = os.path.join(args.saved, os.path.basename(args.input)+'_tmp_probe.fa')
tmppbfaio = open(tmppbfa, 'w')
seqnum = 0
for tmppb in jffilteredprobe:
print('>','seq',seqnum, sep='',file=tmppbfaio)
print(tmppb,file=tmppbfaio)
seqnum += 1
tmppbfaio.close()
del jffilteredprobe
bwafiltedpb = bwa.bwafilter(bwabin=args.bwa, reffile=bwaindex, inputfile=tmppbfa, minas=args.length,
maxxs=int(args.length*args.homology/100), threadnumber=args.threads)
# print(bwafiltedpb)
tmpbwaftlist = os.path.join(args.saved, os.path.basename(args.input)+'.bed')
alltmpbwaftlist = os.path.join(args.saved, os.path.basename(args.input)+'_all.bed')
tmpbwaftlistio = open(tmpbwaftlist,'w')
allbwaftlistio = open(alltmpbwaftlist,'w')
seqlenfile = os.path.join(args.saved, os.path.basename(args.input)+'.len')
seqlenio = open(seqlenfile,'w')
seqlength = bwa.bwareflength(bwabin=args.bwa, reffile=bwaindex)
for seqname in seqlength:
print(seqname, seqlength[seqname], sep='\t', file=seqlenio)
seqlenio.close()
oligobefortmf = list()
for pbtmp in bwafiltedpb:
# print(pbtmp, file=tmpbwaftlistio)
nowpbcounter = dict()
nowpbcounter['seq'] = pbtmp
nowpbcounter['dTm'] = args.dtm
nowpbcounter['rprimer'] = args.primer
oligobefortmf.append(nowpbcounter)
keepedprobe = list()
ctedpb = 0
oligobefortmflen = len(oligobefortmf)
print("oligobefortmflen:",oligobefortmflen)
pbftpool = Pool()
for (pb, keep) in pbftpool.imap_unordered(probefilter, oligobefortmf):
if keep:
keepedprobe.append(pb)
# print(pb, file=tmpbwaftlistio)
ctedpb += 1
if ctedpb % 10000 == 0:
print(ctedpb,'/',oligobefortmflen)
pbdictbychr = dict()
pbftpool.close()
for pb in keepedprobe:
seq, chro, start = pb.split('\t')
start = int(start)
if chro in pbdictbychr:
pbdictbychr[chro][start] = seq
else:
pbdictbychr[chro] = dict()
pbdictbychr[chro][start] = seq
lenrprimer = len(args.primer)
if lenrprimer == 0:
lenrprimer = 5
slidwindow = lenrprimer+args.length
for chro in pbdictbychr:
startn = 0
for startnow in sorted(pbdictbychr[chro]):
endnow = startnow + args.length - 1
print(chro, startnow, endnow, pbdictbychr[chro][startnow],file=allbwaftlistio,sep='\t')
if startnow > startn+slidwindow:
#startn = startnow+slidwindow
startn = startnow
print(chro, startnow, endnow, pbdictbychr[chro][startnow], file=tmpbwaftlistio, sep='\t')
tmpbwaftlistio.close()
allbwaftlistio.close()
print("Job finshed!!")
def run(self):
if self.kmerbuild:
jfcounter = jellyfish.jfcount(jfpath=self.jellyfishpath,
mer=self.kmer,
infile=self.genomefile,
output=self.jfkmerfile,
threads=self.threadsnumber,
lowercount=self.lowercount,
size=self.size)
"""
check jelly fish count run correctly
"""
if jfcounter:
self.progressnumber = self.progressnumber + 5
self.notifyProgress.emit(self.progressnumber)
self.notifyMessage.emit("JellyFish Count finished...")
else:
self.notifyMessage.emit("JellyFish Count Error!!!")
else:
jfcountmess = "Use " + self.jfkmerfile
self.progressnumber = self.progressnumber + 5
self.notifyProgress.emit(self.progressnumber)
self.notifyMessage.emit(jfcountmess)
if self.indexbuild:
if self.aligner == 'BWA':
bwa.bwaindex(self.alnpath, self.genomefile, self.samplefolder)
self.notifyMessage.emit("BWA Index build finished...")
self.progressnumber = self.progressnumber + 5
self.notifyProgress.emit(self.progressnumber)
elif self.aligner == 'BLAT':
"""
add code for BLAT
"""
pass
else:
self.progressnumber = self.progressnumber + 5
self.notifyProgress.emit(self.progressnumber)
"""
load and splite input file
"""
# splite sequence longer than 10M
spsize = 10000000
maxkmerscore = int(self.pblength * self.homology / 100) - self.kmer
jffilteredprobe = list()
fastain = Fasta(self.inputfile)
jffpbrunerlist = list()
for seqname in fastain.keys():
chrlen = len(fastain[seqname])
if chrlen < spsize:
start = 0
end = chrlen - 1
jffpbruner = jellyfish.JFfpbruner(jfpath=self.jellyfishpath,
jfkmerfile=self.jfkmerfile,
mer=self.kmer,
pyfasta=fastain,
seqname=seqname,
pblength=self.pblength,
maxkmerscore=maxkmerscore,
start=start,
end=end,
step=self.step)
jffpbrunerlist.append(jffpbruner)
else:
chrblock = int(chrlen / spsize) + 1
for i in range(chrblock):
start = i * spsize
end = start + spsize - 1
if end >= chrlen:
end = chrlen - 1
jffpbruner = jellyfish.JFfpbruner(
jfpath=self.jellyfishpath,
jfkmerfile=self.jfkmerfile,
mer=self.kmer,
pyfasta=fastain,
seqname=seqname,
pblength=self.pblength,
maxkmerscore=maxkmerscore,
start=start,
end=end,
step=self.step)
jffpbrunerlist.append(jffpbruner)
jffinished = 0
for curpblist in self.pool.imap_unordered(jellyfish.kmerfilterprobe,
jffpbrunerlist):
jffilteredprobe.extend(curpblist)
tmpprogress = float(
format(
self.progressnumber +
(jffinished / len(jffpbrunerlist) * 40), ".2f"))
self.notifyProgress.emit(tmpprogress)
if self.isRunning():
print("running")
else:
print("not running")
jffinished += 1
self.notifyMessage.emit('kmer filter finished!!')
self.progressnumber = 50.0
self.notifyProgress.emit(self.progressnumber)
tmppbfa = os.path.join(
self.samplefolder,
os.path.basename(self.inputfile) + '_tmp_probes.fa')
tmppbfaio = open(tmppbfa, 'w')
seqnum = 0
for tmppb in jffilteredprobe:
print('>', 'seq', seqnum, sep='', file=tmppbfaio)
print(tmppb, file=tmppbfaio)
seqnum += 1
tmppbfaio.close()
#delete jffilteredprobe and release memory
del jffilteredprobe
bwaindexfile = os.path.join(self.samplefolder,
os.path.basename(self.genomefile))
bwafiltedpb = bwa.bwafilter(bwabin=self.alnpath,
reffile=bwaindexfile,
inputfile=tmppbfa,
minas=self.pblength,
maxxs=int(self.pblength * self.homology /
100),
threadnumber=self.threadsnumber)
tmpbwaftlist = os.path.join(self.samplefolder,
os.path.basename(self.inputfile) + '.bed')
alltmpbwaftlist = os.path.join(
self.samplefolder,
os.path.basename(self.inputfile) + '_all.bed')
tmpbwaftlistio = open(tmpbwaftlist, 'w')
allbwaftlistio = open(alltmpbwaftlist, 'w')
seqlenfile = os.path.join(self.samplefolder,
os.path.basename(self.inputfile)) + '.len'
seqlenio = open(seqlenfile, 'w')
seqlength = bwa.bwareflength(bwabin=self.alnpath, reffile=bwaindexfile)
for seqname in seqlength:
print(seqname, seqlength[seqname], sep='\t', file=seqlenio)
seqlenio.close()
oligobefortmf = list()
for pbtmp in bwafiltedpb:
# print(pbtmp, file=tmpbwaftlistio)
nowpbcounter = dict()
nowpbcounter['seq'] = pbtmp
nowpbcounter['dTm'] = self.dTm
nowpbcounter['rprimer'] = self.rprimer
oligobefortmf.append(nowpbcounter)
keepedprobe = list()
self.progressnumber = 55
self.notifyProgress.emit(self.progressnumber)
ctedpb = 0
oligobefortmflen = len(oligobefortmf)
for (pb, keep) in self.pool.imap_unordered(probefilter, oligobefortmf):
if keep:
keepedprobe.append(pb)
# print(pb, file=tmpbwaftlistio)
ctedpb += 1
if ctedpb % 10000 == 0:
tmpprogress = float(
format(
self.progressnumber + (ctedpb / oligobefortmflen * 30),
".2f"))
self.notifyProgress.emit(tmpprogress)
self.notifyProgress.emit(90)
pbdictbychr = dict()
#load pb to dict
for pb in keepedprobe:
# print(pb, file=tmpbwaftlistio)
seq, chro, start = pb.split('\t')
start = int(start)
if chro in pbdictbychr:
pbdictbychr[chro][start] = seq
else:
pbdictbychr[chro] = dict()
pbdictbychr[chro][start] = seq
#get lenth of primer
lenrprimer = len(self.rprimer)
if lenrprimer == 0:
lenrprimer = 5
slidwindow = lenrprimer + self.pblength
for chro in pbdictbychr:
startn = 0
for startnow in sorted(pbdictbychr[chro]):
endnow = startnow + self.pblength - 1
print(chro,
startnow,
endnow,
pbdictbychr[chro][startnow],
file=allbwaftlistio,
sep='\t')
if startnow > startn + slidwindow:
#startn = startnow+slidwindow
startn = startnow
print(chro,
startnow,
endnow,
pbdictbychr[chro][startnow],
file=tmpbwaftlistio,
sep='\t')
tmpbwaftlistio.close()
allbwaftlistio.close()
#remove temp fasta file
# os.remove(tmppbfa)
self.notifyProgress.emit(100)
self.notifyMessage.emit('all finished!!')
def main():
args = check_options(get_options())
genomesize = int(os.path.getsize(args.genome)/1e6)
kmer = int(log(genomesize, 4)+1)
if kmer < 17:
kmer = 17
#jellyfish par
lowercount = 2
#jellyfish par
jfsize = '100M'
# splite sequence longer than 10M
spsize = 10000000
step = args.step
maxkmerscore = int(args.length * args.homology / 100) - kmer
jfpool = Pool(args.threads)
# ?build kmerindex
jfkmerfile = os.path.join(args.saved,(os.path.basename(args.genome)+'_'+str(kmer)+'mer.jf'))
kmerbuild = True
if os.path.isfile(jfkmerfile):
if not args.docker:
print("find:", jfkmerfile)
kmmess = "Found kmerfile "+jfkmerfile+". Do you want rebuild it? Press Y or N to continue:"
print(kmmess)
while True:
char = getch()
if char.lower() in ("y", "n"):
print(char)
if char == 'y':
kmerbuild = True
elif char == 'n':
kmerbuild = False
break
# ?build bwa index
bwaindexfile = os.path.basename(args.genome)
bwatestindex = os.path.join(args.saved, bwaindexfile+'.sa')
bwaindex = os.path.join(args.saved, bwaindexfile)
bwabuild = True
if os.path.isfile(bwatestindex):
if not args.docker:
print('find:', bwatestindex)
bwamess = "Found bwa index file " + bwatestindex + ". Do you want rebuild it? Press Y or N to continue:"
print(bwamess)
while True:
char = getch()
if char.lower() in ("y", "n"):
print(char)
if char == 'y':
bwabuild = True
elif char == 'n':
bwabuild = False
break
print("genomesize:",genomesize, "kmer:",kmer, "jfkmerfile:",
jfkmerfile, "kmerbuild:", kmerbuild, "bwabuild:", bwabuild, "threads:", args.threads)
# Build Jellyfish index
if kmerbuild:
jfcount = jellyfish.jfcount(jfpath=args.jellyfish, mer=kmer, infile=args.genome, output=jfkmerfile,
threads=args.threads, lowercount=lowercount, size=jfsize)
if jfcount:
print("JellyFish Count finished ...")
else:
print("JellyFish Count Error!!!")
sys.exit(1)
else:
print("Use ", jfkmerfile)
# End build Jellyfish index
if bwabuild:
bwa.bwaindex(args.bwa, args.genome, args.saved)
print("bwa index build finished ...")
else:
print("Use", bwatestindex)
jffilteredprobe = list()
fastain = Fasta(args.input)
jffpbrunerlist = list()
for seqname in fastain.keys():
chrlen = len(fastain[seqname])
if chrlen < spsize:
start = 0
end = chrlen - 1
jffpbruner = jellyfish.JFfpbruner(jfpath=args.jellyfish, jfkmerfile=jfkmerfile, mer=kmer,
pyfasta=fastain, seqname=seqname, pblength=args.length,
maxkmerscore=maxkmerscore, start=start,
end=end, step=step)
jffpbrunerlist.append(jffpbruner)
else:
chrblock = int(chrlen/spsize) + 1
for i in range(chrblock):
start = i * spsize
end = start + spsize - 1
if end >= chrlen:
end = chrlen - 1
jffpbruner = jellyfish.JFfpbruner(jfpath=args.jellyfish, jfkmerfile=jfkmerfile, mer=kmer,
pyfasta=fastain, seqname=seqname, pblength=args.length,
maxkmerscore=maxkmerscore, start=start,
end=end, step=step)
jffpbrunerlist.append(jffpbruner)
jffinished = 0
for curpblist in jfpool.imap_unordered(jellyfish.kmerfilterprobe, jffpbrunerlist):
jffilteredprobe.extend(curpblist)
jffinished += 1
print("Jellyfish filter: ",jffinished,'/',len(jffpbrunerlist), sep='')
jfpool.close()
print('Jellyfish filter finished!!')
tmppbfa = os.path.join(args.saved, os.path.basename(args.input)+'_tmp_probe.fa')
tmppbfaio = open(tmppbfa, 'w')
seqnum = 0
for tmppb in jffilteredprobe:
print('>','seq',seqnum, sep='',file=tmppbfaio)
print(tmppb,file=tmppbfaio)
seqnum += 1
tmppbfaio.close()
del jffilteredprobe
bwafiltedpb = bwa.bwafilter(bwabin=args.bwa, reffile=bwaindex, inputfile=tmppbfa, minas=args.length,
maxxs=int(args.length*args.homology/100), threadnumber=args.threads)
# print(bwafiltedpb)
tmpbwaftlist = os.path.join(args.saved, os.path.basename(args.input)+'.bed')
alltmpbwaftlist = os.path.join(args.saved, os.path.basename(args.input)+'_all.bed')
tmpbwaftlistio = open(tmpbwaftlist,'w')
allbwaftlistio = open(alltmpbwaftlist,'w')
seqlenfile = os.path.join(args.saved, os.path.basename(args.input)+'.len')
seqlenio = open(seqlenfile,'w')
seqlength = bwa.bwareflength(bwabin=args.bwa, reffile=bwaindex)
for seqname in seqlength:
print(seqname, seqlength[seqname], sep='\t', file=seqlenio)
seqlenio.close()
oligobefortmf = list()
for pbtmp in bwafiltedpb:
# print(pbtmp, file=tmpbwaftlistio)
nowpbcounter = dict()
nowpbcounter['seq'] = pbtmp
nowpbcounter['dTm'] = args.dtm
nowpbcounter['rprimer'] = args.primer
oligobefortmf.append(nowpbcounter)
keepedprobe = list()
ctedpb = 0
oligobefortmflen = len(oligobefortmf)
print("oligobefortmflen:",oligobefortmflen)
pbftpool = Pool()
for (pb, keep) in pbftpool.imap_unordered(probefilter, oligobefortmf):
if keep:
keepedprobe.append(pb)
# print(pb, file=tmpbwaftlistio)
ctedpb += 1
if ctedpb % 10000 == 0:
print(ctedpb,'/',oligobefortmflen)
pbdictbychr = dict()
pbftpool.close()
for pb in keepedprobe:
seq, chro, start = pb.split('\t')
start = int(start)
if chro in pbdictbychr:
pbdictbychr[chro][start] = seq
else:
pbdictbychr[chro] = dict()
pbdictbychr[chro][start] = seq
lenrprimer = len(args.primer)
if lenrprimer == 0:
lenrprimer = 5
slidwindow = lenrprimer+args.length
for chro in pbdictbychr:
startn = 0
for startnow in sorted(pbdictbychr[chro]):
endnow = startnow + args.length - 1
print(chro, startnow, endnow, pbdictbychr[chro][startnow],file=allbwaftlistio,sep='\t')
if startnow > startn+slidwindow:
#startn = startnow+slidwindow
startn = startnow
print(chro, startnow, endnow, pbdictbychr[chro][startnow], file=tmpbwaftlistio, sep='\t')
tmpbwaftlistio.close()
allbwaftlistio.close()
print("Job finshed!!")
def run(self):
if self.kmerbuild:
jfcounter = jellyfish.jfcount(jfpath=self.jellyfishpath, mer=self.kmer,
infile=self.genomefile, output=self.jfkmerfile, threads=self.threadsnumber,
lowercount=self.lowercount, size=self.size)
"""
check jelly fish count run correctly
"""
if jfcounter:
self.progressnumber = self.progressnumber + 5
self.notifyProgress.emit(self.progressnumber)
self.notifyMessage.emit("JellyFish Count finished...")
else:
self.notifyMessage.emit("JellyFish Count Error!!!")
else:
jfcountmess = "Use " + self.jfkmerfile
self.progressnumber = self.progressnumber + 5
self.notifyProgress.emit(self.progressnumber)
self.notifyMessage.emit(jfcountmess)
if self.indexbuild:
if self.aligner == 'BWA':
bwa.bwaindex(self.alnpath, self.genomefile, self.samplefolder)
self.notifyMessage.emit("BWA Index build finished...")
self.progressnumber = self.progressnumber + 5
self.notifyProgress.emit(self.progressnumber)
elif self.aligner == 'BLAT':
"""
add code for BLAT
"""
pass
else:
self.progressnumber = self.progressnumber + 5
self.notifyProgress.emit(self.progressnumber)
"""
load and splite input file
"""
# splite sequence longer than 10M
spsize = 10000000
maxkmerscore = int(self.pblength * self.homology / 100) - self.kmer
jffilteredprobe = list()
fastain = Fasta(self.inputfile)
jffpbrunerlist = list()
for seqname in fastain.keys():
chrlen = len(fastain[seqname])
if chrlen < spsize:
start = 0
end = chrlen - 1
jffpbruner = jellyfish.JFfpbruner(jfpath=self.jellyfishpath, jfkmerfile=self.jfkmerfile, mer=self.kmer,
pyfasta=fastain, seqname=seqname, pblength=self.pblength,
maxkmerscore=maxkmerscore, start=start,
end=end, step=self.step)
jffpbrunerlist.append(jffpbruner)
else:
chrblock = int(chrlen / spsize) + 1
for i in range(chrblock):
start = i * spsize
end = start + spsize - 1
if end >= chrlen:
end = chrlen - 1
jffpbruner = jellyfish.JFfpbruner(jfpath=self.jellyfishpath, jfkmerfile=self.jfkmerfile, mer=self.kmer,
pyfasta=fastain, seqname=seqname, pblength=self.pblength,
maxkmerscore=maxkmerscore, start=start,
end=end, step=self.step)
jffpbrunerlist.append(jffpbruner)
jffinished = 0
for curpblist in self.pool.imap_unordered(jellyfish.kmerfilterprobe, jffpbrunerlist):
jffilteredprobe.extend(curpblist)
tmpprogress = float(format(self.progressnumber + (jffinished/len(jffpbrunerlist) * 40),".2f"))
self.notifyProgress.emit(tmpprogress)
if self.isRunning():
print("running")
else:
print("not running")
jffinished += 1
self.notifyMessage.emit('jelly fish finished!!')
self.progressnumber = 50.0
self.notifyProgress.emit(self.progressnumber)
tmppbfa = os.path.join(self.samplefolder, os.path.basename(self.inputfile)+'_tmp_probes.fa')
tmppbfaio = open(tmppbfa, 'w')
seqnum = 0
for tmppb in jffilteredprobe:
print('>','seq',seqnum, sep='',file=tmppbfaio)
print(tmppb,file=tmppbfaio)
seqnum += 1
tmppbfaio.close()
#delete jffilteredprobe and release memory
del jffilteredprobe
bwaindexfile = os.path.join(self.samplefolder, os.path.basename(self.genomefile))
bwafiltedpb = bwa.bwafilter(bwabin=self.alnpath, reffile=bwaindexfile, inputfile=tmppbfa, minas=self.pblength,
maxxs=int(self.pblength * self.homology / 100), threadnumber=self.threadsnumber)
tmpbwaftlist = os.path.join(self.samplefolder, os.path.basename(self.inputfile)+'.bed')
alltmpbwaftlist = os.path.join(self.samplefolder, os.path.basename(self.inputfile)+'_all.bed')
tmpbwaftlistio = open(tmpbwaftlist,'w')
allbwaftlistio = open(alltmpbwaftlist,'w')
seqlenfile = os.path.join(self.samplefolder, os.path.basename(self.inputfile))+'.len'
seqlenio = open(seqlenfile, 'w')
seqlength = bwa.bwareflength(bwabin=self.alnpath, reffile=bwaindexfile)
for seqname in seqlength:
print(seqname, seqlength[seqname], sep='\t', file=seqlenio)
seqlenio.close()
oligobefortmf = list()
for pbtmp in bwafiltedpb:
# print(pbtmp, file=tmpbwaftlistio)
nowpbcounter = dict()
nowpbcounter['seq'] = pbtmp
nowpbcounter['dTm'] = self.dTm
nowpbcounter['rprimer'] = self.rprimer
oligobefortmf.append(nowpbcounter)
keepedprobe = list()
self.progressnumber = 55
self.notifyProgress.emit(self.progressnumber)
ctedpb = 0
oligobefortmflen = len(oligobefortmf)
for (pb, keep) in self.pool.imap_unordered(probefilter, oligobefortmf):
if keep:
keepedprobe.append(pb)
# print(pb, file=tmpbwaftlistio)
ctedpb += 1
if ctedpb % 10000 == 0:
tmpprogress = float(format(self.progressnumber + (ctedpb/oligobefortmflen * 30),".2f"))
self.notifyProgress.emit(tmpprogress)
self.notifyProgress.emit(90)
pbdictbychr = dict()
#load pb to dict
for pb in keepedprobe:
# print(pb, file=tmpbwaftlistio)
seq, chro, start = pb.split('\t')
start = int(start)
if chro in pbdictbychr:
pbdictbychr[chro][start] = seq
else:
pbdictbychr[chro] = dict()
pbdictbychr[chro][start] = seq
#get lenth of primer
lenrprimer = len(self.rprimer)
if lenrprimer == 0:
lenrprimer = 5
slidwindow = lenrprimer+self.pblength
for chro in pbdictbychr:
startn = 0
for startnow in sorted(pbdictbychr[chro]):
endnow = startnow + self.pblength - 1
print(chro, startnow, endnow, pbdictbychr[chro][startnow],file=allbwaftlistio,sep='\t')
if startnow > startn+slidwindow:
#startn = startnow+slidwindow
startn = startnow
print(chro, startnow, endnow, pbdictbychr[chro][startnow], file=tmpbwaftlistio, sep='\t')
tmpbwaftlistio.close()
allbwaftlistio.close()
#remove temp fasta file
# os.remove(tmppbfa)
self.notifyProgress.emit(100)
self.notifyMessage.emit('all finished!!')