def blat_getseqlen(par):
sequence = par['sequence']
blatport = par['blatport']
gfcpath = par['gfcpath']
pblength = par['pblength']
file2bit = par['file2bit']
dtm = par['dtm']
minIdentity = par['minIdentity']
st = 0
# pblength = 48
seqlen = len(sequence) - pblength
print(seqlen, blatport, gfcpath, sequence[0:10])
probelist = list()
while st < seqlen:
sp = st+pblength
nowseq = sequence[st:sp]
st += 5
if not nowseq:
continue
if not prefilter.atcg_filter(nowseq, 7):
if 0 < blat.blat_search_sequence(gfcpath, sequence=nowseq, blatport=blatport, minIdentity=minIdentity, file2bit=file2bit) < 2:
if not primer3_filter.primer3_filter(sequence=nowseq, dtm=dtm):
probelist.append(nowseq)
st += pblength
return probelist
def probefilter(nowpbcounter):
sequence, seqname, start = nowpbcounter['seq'].split('\t')
dTm = nowpbcounter['dTm']
rPrimer = nowpbcounter['rprimer']
keep = False
if prefilter.atcg_filter(sequence, 5):
# print(self.sequence, " not pass atcg")
pass
elif dTm == -1:
keep = True
else:
if rPrimer:
if primer3_filter.primer3_filter_withRprimer(sequence, rPrimer, dtm=dTm):
pass
else:
keep = True
else:
if primer3_filter.primer3_filter(sequence, dtm=dTm):
pass
else:
keep = True
return (nowpbcounter['seq'], keep)
def probefilter(nowpbcounter):
sequence, seqname, start = nowpbcounter['seq'].split('\t')
dTm = nowpbcounter['dTm']
rPrimer = nowpbcounter['rprimer']
keep = False
if prefilter.atcg_filter(sequence, 5):
# print(self.sequence, " not pass atcg")
pass
else:
if rPrimer:
if primer3_filter.primer3_filter_withRprimer(sequence, rPrimer, dtm=dTm):
pass
else:
keep = True
else:
if primer3_filter.primer3_filter(sequence, dtm=dTm):
pass
else:
keep = True
return (nowpbcounter['seq'], keep)
