def build_fwtrack_v2(self, teIdx):
"""Build FWTrackII from all lines, return a FWTrackII object.
Note only the unique match for a tag is kept.
"""
fwtrack = FWTrackII(filename=self.__srcfile)
fseek = self.fhd.seek
fread = self.fhd.read
ftell = self.fhd.tell
references = []
# move to pos 4, get the length of header
fseek(4)
header_len = struct.unpack('<i', fread(4))[0]
fseek(header_len + ftell())
# get the number of chromosome
nc = struct.unpack('<i', fread(4))[0]
for x in range(nc):
# read each chromosome name
nlength = struct.unpack('<i', fread(4))[0]
chrname = fread(nlength)[:-1]
references.append(chrname)
# jump over chromosome size, we don't need it
fseek(ftell() + 4)
i = 0
m = 0
multi_reads = []
prev_seq = ""
seq_len = 0
seq_len_count = 0
while 1:
try:
entrylength = struct.unpack('<i', fread(4))[0]
except struct.error:
break
(seq_name, chrid, fpos, flen, strand,
qual) = self.__binary_parse(fread(entrylength))
if seq_len_count < 1000:
seq_len += flen
seq_len_count += 1
i += 1
if i == 1000000:
m += 1
logging.info(" %d" % (m * 1000000))
i = 0
if fpos >= 0:
if seq_name == prev_seq: #multi reads
r = Read()
r.chrom = references[chrid]
if strand == 1:
r.strand = 1
r.start = fpos - flen
r.end = fpos
else:
r.start = fpos
r.end = fpos + flen
r.strand = 0
r.name = seq_name
r.weight = 0
r.qual = qual
multi_reads.append(r)
else:
if prev_seq != "":
(sel_reads, w) = self.sameFam(multi_reads, teIdx)
# w = 1.0/len(multi_reads)
for k in range(len(sel_reads)):
rr = sel_reads[k]
#w = weights[k]
# w = round(1.0/len(multi_reads),2)
#for k in range(len(multi_reads)) :
# rr = multi_reads[k]
fwtrack.add_loc(rr.chrom, rr.start, rr.strand, w)
multi_reads = []
prev_seq = seq_name
r = Read()
r.chrom = references[chrid]
if strand == 1:
r.strand = 1
r.start = fpos - flen
r.end = fpos
else:
r.start = fpos
r.end = fpos + flen
r.strand = 0
r.name = seq_name
r.qual = qual
multi_reads.append(r)
if len(multi_reads) > 0:
(sel_reads, w) = self.sameFam(multi_reads, teIdx)
# w = 1.0/len(multi_reads)
for k in range(len(sel_reads)):
rr = sel_reads[k]
#w = weights[k]
#w = round(1.0/len(multi_reads),2)
#for k in range(len(multi_reads)) :
# rr = multi_reads[k]
fwtrack.add_loc(rr.chrom, rr.start, rr.strand, w)
self.fhd.close()
if seq_len_count > 0:
fwtrack.setTsize(int(seq_len / seq_len_count))
self.__buildAready = True
return fwtrack
def build_fwtrack_v2 (self,teIdx):
"""Build FWTrackII from all lines, return a FWTrackII object.
Note only the unique match for a tag is kept.
"""
fwtrack = FWTrackII(filename=self.__srcfile)
fseek = self.fhd.seek
fread = self.fhd.read
ftell = self.fhd.tell
references = []
# move to pos 4, get the length of header
fseek(4)
header_len = struct.unpack('<i', fread(4))[0]
fseek(header_len + ftell())
# get the number of chromosome
nc = struct.unpack('<i', fread(4))[0]
for x in range(nc):
# read each chromosome name
nlength = struct.unpack('<i', fread(4))[0]
chrname = fread(nlength)[:-1]
references.append(chrname)
# jump over chromosome size, we don't need it
fseek(ftell() + 4)
i = 0
m = 0
multi_reads = []
prev_seq = ""
seq_len = 0
seq_len_count = 0
while 1:
try:
entrylength = struct.unpack('<i', fread(4))[0]
except struct.error:
break
(seq_name,chrid,fpos,flen,strand,qual) = self.__binary_parse(fread(entrylength))
if seq_len_count < 1000 :
seq_len += flen
seq_len_count += 1
i+=1
if i == 1000000:
m += 1
logging.info(" %d" % (m*1000000))
i=0
if fpos >= 0:
if seq_name == prev_seq : #multi reads
r = Read()
r.chrom = references[chrid]
if strand == 1 :
r.strand = 1
r.start = fpos - flen
r.end = fpos
else :
r.start = fpos
r.end = fpos + flen
r.strand = 0
r.name = seq_name
r.weight = 0
r.qual = qual
multi_reads.append(r)
else :
if prev_seq != "" :
(sel_reads,w) = self.sameFam(multi_reads,teIdx)
# w = 1.0/len(multi_reads)
for k in range(len(sel_reads)) :
rr = sel_reads[k]
#w = weights[k]
# w = round(1.0/len(multi_reads),2)
#for k in range(len(multi_reads)) :
# rr = multi_reads[k]
fwtrack.add_loc(rr.chrom,rr.start,rr.strand,w)
multi_reads = []
prev_seq = seq_name
r = Read()
r.chrom = references[chrid]
if strand == 1 :
r.strand = 1
r.start = fpos - flen
r.end = fpos
else :
r.start = fpos
r.end = fpos + flen
r.strand = 0
r.name = seq_name
r.qual = qual
multi_reads.append(r)
if len(multi_reads) > 0 :
(sel_reads,w) = self.sameFam(multi_reads,teIdx)
# w = 1.0/len(multi_reads)
for k in range(len(sel_reads)) :
rr = sel_reads[k]
#w = weights[k]
#w = round(1.0/len(multi_reads),2)
#for k in range(len(multi_reads)) :
# rr = multi_reads[k]
fwtrack.add_loc(rr.chrom,rr.start,rr.strand,w)
self.fhd.close()
if seq_len_count > 0 :
fwtrack.setTsize(int(seq_len/seq_len_count))
self.__buildAready = True
return fwtrack
def build_fwtrack_v2(self, teIdx):
fwtrack = FWTrackII(filename=self.__srcfile)
i = 0
m = 0
pre_seq_name = ""
multi_reads = []
seq_len_count = 0
seq_len = 0
# cnt = 0
strand = 0
try:
f = open(self.__srcfile, 'r')
except IOError:
logging.error("open file %s error !\n" % (self.__srcfile))
sys.exit(1)
else:
for line in f:
# Go through bed file and assign each line to corresponding file.
line = line.strip()
items = line.split('\t')
chrname = items[0]
if seq_len_count < 1000:
seq_len += int(items[2]) - int(items[1])
seq_len_count += 1
i += 1
start = 0
if i == 1000000:
m += 1
logging.info(" %d" % (m * 1000000))
i = 0
if items[5] == "+":
strand = 0
start = int(items[1])
end = int(items[2])
else:
strand = 1
start = int(items[2])
w = 1.0
if len(items) > 6: #there is weight assigned to each alignment
w = float(items[6])
# self.size += w
fwtrack.add_loc(chrname, start, strand, w)
else:
if pre_seq_name == "":
pre_seq_name = items[3]
r = Read()
r.chrom = chrname
r.start = start
r.strand = strand
if pre_seq_name == items[3]:
multi_reads.append(r)
else:
(sel_reads, w) = self.sameFam(multi_reads, teIdx,
pre_seq_name)
# w = 1.0/len(multi_reads)
for k in range(len(sel_reads)):
read = sel_reads[k]
#w = weights[k]
fwtrack.add_loc(read.chrom, read.start,
read.strand, w)
#self.size
multi_reads = []
pre_seq_name = items[3]
multi_reads.append(r)
# else:
# logging.warn("Unspecified chromosome name at %s line: %s. Skip!\n" %(self.__srcfile,line))
if len(multi_reads) > 0:
# w = float(1.0/len(multi_reads))
#for k in range(len(multi_reads)) :
# read = multi_reads[k]
(sel_reads, w) = self.sameFam(multi_reads, teIdx)
# w = 1.0/len(multi_reads)
for k in range(len(sel_reads)):
read = sel_reads[k]
#w = weights[k]
fwtrack.add_loc(read.chrom, read.start, read.strand, w)
f.close()
if seq_len_count > 0:
fwtrack.setTsize(int(seq_len / seq_len_count))
fwtrack.sort()
self.__buildAready = True
return fwtrack
def build_fwtrack_v2 (self,teIdx):
fwtrack = FWTrackII(filename=self.__srcfile)
i = 0
m = 0
pre_seq_name = ""
multi_reads = []
seq_len_count = 0
seq_len = 0
# cnt = 0
strand = 0
try:
f = open(self.__srcfile,'r')
except IOError:
logging.error("open file %s error !\n" %(self.__srcfile))
sys.exit(1)
else:
for line in f:
# Go through bed file and assign each line to corresponding file.
line = line.strip()
items = line.split('\t')
chrname = items[0]
if seq_len_count < 1000 :
seq_len += int(items[2]) - int(items[1])
seq_len_count += 1
i+=1
start = 0
if i == 1000000:
m += 1
logging.info(" %d" % (m*1000000))
i=0
if items[5] == "+" :
strand = 0
start = int(items[1])
end = int(items[2])
else :
strand = 1
start = int(items[2])
w = 1.0
if len(items) > 6 : #there is weight assigned to each alignment
w = float(items[6])
# self.size += w
fwtrack.add_loc(chrname,start,strand,w)
else :
if pre_seq_name == "" :
pre_seq_name = items[3]
r = Read()
r.chrom = chrname
r.start = start
r.strand = strand
if pre_seq_name == items[3] :
multi_reads.append(r)
else :
(sel_reads,w) = self.sameFam(multi_reads,teIdx,pre_seq_name)
# w = 1.0/len(multi_reads)
for k in range(len(sel_reads)) :
read = sel_reads[k]
#w = weights[k]
fwtrack.add_loc(read.chrom,read.start,read.strand,w)
#self.size
multi_reads = []
pre_seq_name = items[3]
multi_reads.append(r)
# else:
# logging.warn("Unspecified chromosome name at %s line: %s. Skip!\n" %(self.__srcfile,line))
if len(multi_reads) > 0 :
# w = float(1.0/len(multi_reads))
#for k in range(len(multi_reads)) :
# read = multi_reads[k]
(sel_reads,w) = self.sameFam(multi_reads,teIdx)
# w = 1.0/len(multi_reads)
for k in range(len(sel_reads)) :
read = sel_reads[k]
#w = weights[k]
fwtrack.add_loc(read.chrom,read.start,read.strand,w)
f.close()
if seq_len_count > 0 :
fwtrack.setTsize(int(seq_len/seq_len_count))
fwtrack.sort()
self.__buildAready = True
return fwtrack
