def populate(self, filehandle):
# print "populating " + str(self)
# print "seeking to " + str(self.fileLocation)
filehandle.seek(self.fileLocation)
if self.debug:
sys.stderr.write("populating " + str(self) + "\n")
for line in filehandle:
# get next element
line = line.strip()
if self.debug:
sys.stderr.write("\t" + "current line is " + str(line) + "\n")
line = line.strip()
if line == "":
continue
e = parseWigString(line)
# we're done if we've left this block's chrom, or if we've moved beyond
# the end of this blocks boundary.
if e.chrom != self.chrom or e.start > self.end:
break
self.data.append(e)
if self.debug:
sys.stderr.write("built tree for " + str(self) + "\n")
if len(self.data) == 0:
print "empty! --> " + str(self)
self.iTree = IntervalTree(self.data, openEnded=True)
def populate(self, filehandle):
#print "populating " + str(self)
#print "seeking to " + str(self.fileLocation)
filehandle.seek(self.fileLocation)
if self.debug:
sys.stderr.write("populating " + str(self) + "\n")
for line in filehandle:
# get next element
line = line.strip()
if self.debug:
sys.stderr.write("\t" + "current line is " + str(line) + "\n")
line = line.strip()
if line == "":
continue
e = parseWigString(line)
# we're done if we've left this block's chrom, or if we've moved beyond
# the end of this blocks boundary.
if e.chrom != self.chrom or e.start > self.end:
break
self.data.append(e)
if self.debug:
sys.stderr.write("built tree for " + str(self) + "\n")
if len(self.data) == 0:
print "empty! --> " + str(self)
self.iTree = IntervalTree(self.data, openEnded=True)
def regularWigIterator(fd, verbose=False, sortedby=None, scoreType=int):
"""
@param sortedBy: if not None, should be one of ITERATOR_SORTED_BY_START
indicating an order that the input stream must be
sorted in
@raise WigIteratorError: if sortedBy is set and stream is not sorted
"""
if verbose:
try:
totalLines = linesInFile(fd)
pind = ProgressIndicator(totalToDo=totalLines,
messagePrefix="completed",
messageSuffix="of processing " +
getFDName(fd))
except AttributeError:
sys.stderr.write("WigIterator -- warning: " +
"unable to show progress for stream")
verbose = False
chromsSeen = set()
prev = None
fh = openFD(fd)
for line in fh:
if verbose:
pind.done += 1
pind.showProgress()
line = line.strip()
if line == "":
continue
e = parseWigString(line, scoreType=scoreType)
# on same chrom as the prev item, make sure order is right
if prev is not None and sortedby is not None and e.chrom == prev.chrom:
if sortedby == ITERATOR_SORTED_START and prev.start > e.start:
raise WigIteratorError(
"bed file " + fd.name +
" not sorted by start index - saw item " + str(prev) +
" before " + str(e))
# starting a new chrom.. make sure we haven't already seen it
if prev is not None and prev.chrom != e.chrom:
if (sortedby == ITERATOR_SORTED_START) and\
(e.chrom in chromsSeen or prev.chrom > e.chrom):
raise WigIteratorError("BED file " + fd.name +
" not sorted by chrom")
chromsSeen.add(e.chrom)
# all good..
yield e
prev = e
def regularWigIterator(fd, verbose=False, sortedby=None, scoreType=int):
"""
@param sortedBy: if not None, should be one of ITERATOR_SORTED_BY_START
indicating an order that the input stream must be
sorted in
@raise WigIteratorError: if sortedBy is set and stream is not sorted
"""
if verbose:
try:
totalLines = linesInFile(fd)
pind = ProgressIndicator(totalToDo=totalLines,
messagePrefix="completed",
messageSuffix="of processing " + getFDName(fd))
except AttributeError:
sys.stderr.write("WigIterator -- warning: "
+ "unable to show progress for stream")
verbose = False
chromsSeen = set()
prev = None
fh = openFD(fd)
for line in fh:
if verbose:
pind.done += 1
pind.showProgress()
line = line.strip()
if line == "":
continue
e = parseWigString(line, scoreType=scoreType)
# on same chrom as the prev item, make sure order is right
if prev is not None and sortedby is not None and e.chrom == prev.chrom:
if sortedby == ITERATOR_SORTED_START and prev.start > e.start:
raise WigIteratorError("bed file " + fd.name
+ " not sorted by start index - saw item "
+ str(prev) + " before " + str(e))
# starting a new chrom.. make sure we haven't already seen it
if prev is not None and prev.chrom != e.chrom:
if (sortedby == ITERATOR_SORTED_START) and\
(e.chrom in chromsSeen or prev.chrom > e.chrom):
raise WigIteratorError("BED file " + fd.name
+ " not sorted by chrom")
chromsSeen.add(e.chrom)
# all good..
yield e
prev = e
def testRecall(self):
"""
@summary: here we're just testing that we can get back what we put in
to the IndexedWig object in a random order
"""
debug = False
infh = DummyInputStream("\n".join(self.input))
answers = [parseWigString(l) for l in self.input if l.strip() != ""]
shuffle(answers)
iwig = IndexedWig(infh, 2, 2, debug, verbose=False)
if debug:
sys.stderr.write("iwig structure is: \n" + str(iwig) + "\n")
print "done"
for e in answers:
ans = iwig.lookup(e.chrom, e.start)
if debug:
sys.stderr.write("expect: " + str(e.score) + ", got: " + str(ans) + "\n")
assert e.score == ans.score
def testRecall(self):
"""
@summary: here we're just testing that we can get back what we put in
to the IndexedWig object in a random order
"""
debug = False
infh = DummyInputStream("\n".join(self.input))
answers = [parseWigString(l) for l in self.input if l.strip() != ""]
shuffle(answers)
iwig = IndexedWig(infh, 2, 2, debug, verbose=False)
if debug:
sys.stderr.write("iwig structure is: \n" + str(iwig) + "\n")
print "done"
for e in answers:
ans = iwig.lookup(e.chrom, e.start)
if debug:
sys.stderr.write("expect: " + str(e.score) + ", got: " +
str(ans) + "\n")
assert (e.score == ans.score)
def build(self):
currentBlock = None
at = self.handle.tell()
seenChroms = set()
lastIndexSeen = -1
if self.verbose:
try:
pind = ProgressIndicator(
totalToDo=os.path.getsize(self.handle.name),
messagePrefix="completed",
messageSuffix="of building index for " + self.handle.name,
)
except:
sys.stderr.write("IndexedWig -- warning: " + "unable to show progress for stream\n")
self.verbose = False
### note, for loop seems to buffer the file and so tell() gives a
### location that is not where the current line was read from, so
### we stick to readline instead.
rline = None
while rline != "":
# get the next element
rline = self.handle.readline()
line = rline.strip()
if line == "":
continue
e = parseWigString(line)
# keep track of what chroms we've seen for checking order
if not e.chrom in seenChroms:
seenChroms.add(e.chrom)
lastIndexSeen = -1
# check chrom order is ok
for seenChrom in seenChroms:
if seenChrom > e.chrom:
msg = (
"wig file is not sorted, entry for chrom "
+ str(seenChrom)
+ " appears after entry for "
+ str(e.chrom)
)
raise IndexedWigError(msg)
# check position order is ok
if e.start < lastIndexSeen:
msg = (
"wig file is not sorted, entry for chrom "
+ str(e.chrom)
+ " at "
+ str(e.start)
+ " appears after "
+ str(lastIndexSeen)
)
raise IndexedWigError(msg)
# update the last index we've seen
lastIndexSeen = e.end
# debugging message if the current block is full
if self.debug is True:
sys.stderr.write("processing " + str(e))
if currentBlock is not None:
sys.stderr.write("; is current block full?" + str(currentBlock.isfull()) + "\n")
else:
sys.stderr.write("\n")
# we might need to make a new block for this element
if currentBlock is None or currentBlock.isfull() or currentBlock.chrom != e.chrom:
if self.debug:
sys.stderr.write("making new block with " + str(e) + "\n")
if currentBlock is not None:
if self.debug:
sys.stderr.write("closed block: " + str(currentBlock) + "\n")
if currentBlock.chrom not in self.blocksByChrom:
self.blocksByChrom[currentBlock.chrom] = []
self.blocksByChrom[currentBlock.chrom].append(currentBlock)
currentBlock = WigBlock(at, e, self.blocksize)
# add the element to the current block
currentBlock.add(e)
at = self.handle.tell()
if self.verbose:
pind.done = self.handle.tell()
pind.showProgress()
# don't forget to add the final block
if currentBlock != None:
if self.debug:
sys.stderr.write("closed block: " + str(currentBlock) + "\n")
if currentBlock.chrom not in self.blocksByChrom:
self.blocksByChrom[currentBlock.chrom] = []
self.blocksByChrom[currentBlock.chrom].append(currentBlock)
# build the interval trees
for chrom in self.blocksByChrom:
self.itrees[chrom] = IntervalTree(self.blocksByChrom[chrom], openEnded=True)
def build(self):
currentBlock = None
at = self.handle.tell()
seenChroms = set()
lastIndexSeen = -1
if self.verbose:
try:
pind = ProgressIndicator(
totalToDo=os.path.getsize(self.handle.name),
messagePrefix="completed",
messageSuffix="of building index for " + self.handle.name)
except:
sys.stderr.write("IndexedWig -- warning: " +
"unable to show progress for stream\n")
self.verbose = False
### note, for loop seems to buffer the file and so tell() gives a
### location that is not where the current line was read from, so
### we stick to readline instead.
rline = None
while rline != "":
# get the next element
rline = self.handle.readline()
line = rline.strip()
if line == "": continue
e = parseWigString(line)
# keep track of what chroms we've seen for checking order
if not e.chrom in seenChroms:
seenChroms.add(e.chrom)
lastIndexSeen = -1
# check chrom order is ok
for seenChrom in seenChroms:
if seenChrom > e.chrom:
msg = "wig file is not sorted, entry for chrom " + str(seenChrom) +\
" appears after entry for " + str(e.chrom)
raise IndexedWigError(msg)
# check position order is ok
if e.start < lastIndexSeen:
msg = "wig file is not sorted, entry for chrom " + str(e.chrom) +\
" at " + str(e.start) + " appears after " + str(lastIndexSeen)
raise IndexedWigError(msg)
# update the last index we've seen
lastIndexSeen = e.end
# debugging message if the current block is full
if self.debug is True:
sys.stderr.write("processing " + str(e))
if currentBlock is not None:
sys.stderr.write("; is current block full?" +
str(currentBlock.isfull()) + "\n")
else:
sys.stderr.write("\n")
# we might need to make a new block for this element
if currentBlock is None or currentBlock.isfull() or \
currentBlock.chrom != e.chrom:
if self.debug:
sys.stderr.write("making new block with " + str(e) + "\n")
if currentBlock is not None:
if self.debug:
sys.stderr.write("closed block: " + str(currentBlock) +
"\n")
if currentBlock.chrom not in self.blocksByChrom:
self.blocksByChrom[currentBlock.chrom] = []
self.blocksByChrom[currentBlock.chrom].append(currentBlock)
currentBlock = WigBlock(at, e, self.blocksize)
# add the element to the current block
currentBlock.add(e)
at = self.handle.tell()
if self.verbose:
pind.done = self.handle.tell()
pind.showProgress()
# don't forget to add the final block
if currentBlock != None:
if self.debug:
sys.stderr.write("closed block: " + str(currentBlock) + "\n")
if currentBlock.chrom not in self.blocksByChrom:
self.blocksByChrom[currentBlock.chrom] = []
self.blocksByChrom[currentBlock.chrom].append(currentBlock)
# build the interval trees
for chrom in self.blocksByChrom:
self.itrees[chrom] = IntervalTree(self.blocksByChrom[chrom],
openEnded=True)
