def build_fwtrack(self):
"""Build FWTrackII from all lines, return a FWTrackII object.
Note: All locations will be merged (exclude the same
location) then sorted after the track is built.
If both_strand is True, it will store strand information in
FWTrackII object.
if do_merge is False, it will not merge the same location after
the track is built.
"""
fwtrack = FWTrackII()
i = 0
m = 0
for thisline in self.fhd:
(chromosome, fpos, strand) = self.__fw_parse_line(thisline)
i += 1
if i == 1000000:
m += 1
logging.info(" %d" % (m * 1000000))
i = 0
if not fpos or not chromosome:
continue
fwtrack.add_loc(chromosome, fpos, strand)
return fwtrack
def build_fwtrack (self):
"""Build FWTrackII from all lines, return a FWTrackII object.
Note: All locations will be merged (exclude the same
location) then sorted after the track is built.
If both_strand is True, it will store strand information in
FWTrackII object.
if do_merge is False, it will not merge the same location after
the track is built.
"""
fwtrack = FWTrackII()
i = 0
m = 0
for thisline in self.fhd:
(chromosome,fpos,strand) = self.__fw_parse_line(thisline)
i+=1
if i == 1000000:
m += 1
logging.info(" %d" % (m*1000000))
i=0
if not fpos or not chromosome:
continue
fwtrack.add_loc(chromosome,fpos,strand)
return fwtrack
def build_fwtrack(self, dist=200):
"""Build FWTrackII from all lines, return a FWTrackII object.
lfhd: the filehandler for left tag file
rfhd: the filehandler for right tag file
dist: the best distance between two tags in a pair
The score system for pairing two tags:
score = abs(abs(rtag-ltag)-200)+error4lefttag+error4righttag
the smaller score the better pairing. If the score for a
pairing is bigger than 200, this pairing will be discarded.
Note only the best pair is kept. If there are over two best
pairings, this pair of left and right tags will be discarded.
Note, the orders in left tag file and right tag file must
match, i.e., the Nth left tag must has the same name as the
Nth right tag.
Note, remove comment lines beforehand.
"""
fwtrack = FWTrackII()
i = 0
m = 0
lnext = self.lfhd.next
rnext = self.rfhd.next
self.dist = dist
try:
while 1:
lline = lnext()
rline = rnext()
(chromname, fpos, strand) = self.__fw_parse_line(lline, rline)
i += 1
if i == 1000000:
m += 1
logging.info(" %d" % (m * 1000000))
i = 0
if not fpos or not chromname:
continue
try:
chromname = chromname[:chromname.rindex(".fa")]
except ValueError:
pass
fwtrack.add_loc(chromname, fpos, strand)
except StopIteration:
pass
return fwtrack
def build_fwtrack (self, dist=200):
"""Build FWTrackII from all lines, return a FWTrackII object.
lfhd: the filehandler for left tag file
rfhd: the filehandler for right tag file
dist: the best distance between two tags in a pair
The score system for pairing two tags:
score = abs(abs(rtag-ltag)-200)+error4lefttag+error4righttag
the smaller score the better pairing. If the score for a
pairing is bigger than 200, this pairing will be discarded.
Note only the best pair is kept. If there are over two best
pairings, this pair of left and right tags will be discarded.
Note, the orders in left tag file and right tag file must
match, i.e., the Nth left tag must has the same name as the
Nth right tag.
Note, remove comment lines beforehand.
"""
fwtrack = FWTrackII()
i = 0
m = 0
lnext = self.lfhd.next
rnext = self.rfhd.next
self.dist = dist
try:
while 1:
lline = lnext()
rline = rnext()
(chromname,fpos,strand) = self.__fw_parse_line(lline,rline)
i+=1
if i == 1000000:
m += 1
logging.info(" %d" % (m*1000000))
i=0
if not fpos or not chromname:
continue
try:
chromname = chromname[:chromname.rindex(".fa")]
except ValueError:
pass
fwtrack.add_loc(chromname,fpos,strand)
except StopIteration:
pass
return fwtrack
def build_fwtrack(self):
"""Build FWTrackII from all lines, return a FWTrackII object.
"""
fwtrack = FWTrackII()
i = 0
m = 0
for thisline in self.fhd:
(chromosome, fpos, strand) = self.__fw_parse_line(thisline)
i += 1
if i == 1000000:
m += 1
logging.info(" %d" % (m * 1000000))
i = 0
if not fpos or not chromosome:
continue
fwtrack.add_loc(chromosome, fpos, strand)
return fwtrack
def build_fwtrack (self):
"""Build FWTrackII from all lines, return a FWTrackII object.
"""
fwtrack = FWTrackII()
i = 0
m = 0
for thisline in self.fhd:
(chromosome,fpos,strand) = self.__fw_parse_line(thisline)
i+=1
if i == 1000000:
m += 1
logging.info(" %d" % (m*1000000))
i=0
if not fpos or not chromosome:
continue
fwtrack.add_loc(chromosome,fpos,strand)
return fwtrack
def build_fwtrack(self):
"""Build FWTrackII from all lines, return a FWTrackII object.
Note only the unique match for a tag is kept.
"""
fwtrack = FWTrackII()
i = 0
m = 0
references = []
fseek = self.fhd.seek
fread = self.fhd.read
ftell = self.fhd.tell
# move to pos 4, there starts something
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]
references.append(fread(nlength)[:-1])
# jump over chromosome size, we don't need it
fseek(ftell() + 4)
while 1:
try:
entrylength = struct.unpack('<i', fread(4))[0]
except struct.error:
break
(chrid, fpos, strand) = self.__fw_binary_parse(fread(entrylength))
i += 1
if i == 1000000:
m += 1
logging.info(" %d" % (m * 1000000))
i = 0
if fpos >= 0:
fwtrack.add_loc(references[chrid], fpos, strand)
self.fhd.close()
return fwtrack
def build_fwtrack (self):
"""Build FWTrackII from all lines, return a FWTrackII object.
Note only the unique match for a tag is kept.
"""
fwtrack = FWTrackII()
i = 0
m = 0
references = []
fseek = self.fhd.seek
fread = self.fhd.read
ftell = self.fhd.tell
# move to pos 4, there starts something
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]
references.append(fread(nlength)[:-1])
# jump over chromosome size, we don't need it
fseek(ftell() + 4)
while 1:
try:
entrylength = struct.unpack('<i', fread(4))[0]
except struct.error:
break
(chrid,fpos,strand) = self.__fw_binary_parse(fread(entrylength))
i+=1
if i == 1000000:
m += 1
logging.info(" %d" % (m*1000000))
i=0
if fpos >= 0:
fwtrack.add_loc(references[chrid],fpos,strand)
self.fhd.close()
return fwtrack
