def main():
args = check_options(get_options())
try:
probe = pd.read_table(args.input,names=("chrom","start","end","sequence","score","strand"),
dtype={"chrom":str,"start":int,"end":int,"sequence":str,"score":int,"strand":str})
ftprobe = probe[((probe.score > args.mink) & (probe.score < args.maxk) & (
probe.score > probe.score.quantile(args.minquantile)) & (
probe.score < probe.score.quantile(args.maxquantile)))]
probe = ''
chromnames = ftprobe.chrom.unique()
outio = open(args.output, 'w')
for chrom in chromnames:
prestart = 0
strandfr = 1
for index, row in ftprobe[ftprobe.chrom == chrom].sort_values(by='start').iterrows():
nowpbstart = row.start
if nowpbstart > prestart + args.dis:
if args.strand == True:
if strandfr % 2 == 0:
row[5] = '-'
row[3] = revcom(row[3])
strandfr += 1
prestart = nowpbstart
print(row.chrom, row.start, row.end, row.sequence, row.score, row.strand, sep='\t', file=outio)
outio.close()
print("Filtered finished!")
except:
print("Probe file format error. Please check your probe file!")
sys.exit(1)
def getconsensus(bcftoolspath,
bcffile,
chrom,
start,
end,
seq,
sample,
strand='+'):
"""
get consensus by using bcftools
"""
bcftoolspath = subprocesspath.subprocesspath(bcftoolspath)
bcffile = subprocesspath.subprocesspath(bcffile)
mathlen = len(seq) - 10
if mathlen < 10:
mathlen = len(seq)
seqlen = str(mathlen)
pat = re.compile('[ATCG]{' + seqlen + ',}')
if strand == '-':
seq = revcom.revcom(seq)
fastring = '\'>' + chrom + ':' + start + '-' + end + '\\n' + seq + '\''
bcfcon_command = ' '.join([
'echo', fastring, '|' + bcftoolspath + ' consensus -s', sample, bcffile
])
consensus = 'N' * len(seq)
try:
p = Popen(bcfcon_command, shell=True, stdin=PIPE, stdout=PIPE)
for i in p.stdout:
i = i.decode('utf-8').rstrip('\n')
# print(i)
if pat.search(i):
consensus = pat.search(i)[0]
except:
print("warnning: ", bcfcon_command, " ##")
# print('c:',consensus)
return str(consensus)
def probestrtoconsensus(bcfconsensusruner):
(chrom, start, end, seq, score,
strand) = str(bcfconsensusruner.probestr).rstrip().split("\t")
if strand == '-':
seq = revcom.revcom(seq)
strand = '+'
consensusprobe = getconsensus(bcftoolspath=bcfconsensusruner.bcftoolspath,
bcffile=bcfconsensusruner.bcffile,
chrom=chrom,
start=start,
end=end,
seq=seq,
sample=bcfconsensusruner.sample)
res = dict()
res['probestr'] = bcfconsensusruner.probestr
res['consensusprobe'] = consensusprobe
return res
def saveProbe(self):
rowcount = self.tableWidget.rowCount()
if not self.label_prodir.text():
self.setProjetDir()
for i in range(rowcount):
itchr = self.tableWidget.item(i, 0).text()
itstart = int(self.tableWidget.item(i, 1).text())
itend = int(self.tableWidget.item(i, 2).text())
itcolor = self.tableWidget.item(i, 3).text()
#choosed probe number
itsp = int(self.tableWidget.item(i, 5).text())
itstrand = self.tableWidget.item(i, 8).text()
print(itsp)
nowprobes = self.probes[self.probes.Chr == itchr]
nowprobes = nowprobes[nowprobes.Kb > itstart]
nowprobes = nowprobes[nowprobes.Kb < itend]
nowprobes = nowprobes.loc[sample(list(nowprobes.index), itsp)]
nowprobes = nowprobes.drop('Kb', axis=1)
if self.bedformat == 6:
nowprobes = nowprobes.drop('Keep', axis=1)
nowprobes = nowprobes.drop('Kmerscore', axis=1)
outfilename = itcolor + '_' + itchr + '_' + str(
itstart) + '_' + str(itend) + '.bed'
absfile = os.path.join(self.projectdir, outfilename)
nowprobes['Length'] = nowprobes.Seq.map(len)
if itstrand == '-':
revcomseq = nowprobes.Seq.map(revcom)
nowprobes.Seq = revcomseq
nowprobes['Strand'] = ['-'] * len(nowprobes.Seq)
if itstrand == '+':
nowprobes['Strand'] = ['+'] * len(nowprobes.Seq)
if itstrand == 'Both':
newseq = list()
starndlist = list()
strandnow = 0
for seq in nowprobes.Seq:
# seq = nowprobes.iloc[idx].Seq
# print(idx, seq)
if strandnow % 2 == 0:
starndlist.append('+')
newseq.append(seq)
else:
starndlist.append('-')
newseq.append(revcom(seq))
strandnow += 1
nowprobes.Seq = newseq
nowprobes['Strand'] = starndlist
nowprobes.to_csv(path_or_buf=absfile,
sep='\t',
index=False,
index_label=False,
header=False)