def fixedWigIterator(fd, verbose=False, sortedby=None, scoreType=int):
"""
@summary:
"""
fh = openFD(fd)
if verbose:
try:
pind = ProgressIndicator(totalToDo=os.path.getsize(fh.name),
messagePrefix="completed",
messageSuffix="of processing " + fh.name)
except AttributeError:
sys.stderr.write("WigIterator -- warning: "
+ "unable to show progress for stream")
verbose = False
chromsSeen = set()
prev = None
# NUMBERS = set(['1','2','3','4','5','6','7','8','9','0','.'])
currentChrom, at, step = None, None, None
for line in fh:
line = line.strip()
if line == "":
continue
if line[0] == 't' or line[0] == 'f':
parts = line.split()
if parts[0] == "track":
continue
elif parts[0] == "fixedStep":
currentChrom = parts[1].split("=")[1]
at = int(parts[2].split("=")[1])
step = int(parts[3].split("=")[1])
else:
val = float(line)
e = GenomicInterval(currentChrom, at, at + step, None,
val, 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("Wig 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("Wig file " + fd.name
+ " not sorted by chrom")
chromsSeen.add(e.chrom)
# all good..
yield e
prev = e
at += step
if verbose :
pind.done = fh.tell()
pind.showProgress()
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 wigIterator(fd, verbose=False, sortedby=None, scoreType=int):
# peak at the first line to see if it's a regular wig, or
# fixed-step wig
fh = openFD(fd)
at = fh.tell()
line = None
while(line is None):
l = fh.readline()
if l.strip() != "":
line = l
fh.seek(at)
if line.split()[0] == "fixedStep":
return fixedWigIterator(fd, verbose, sortedby)
else:
return regularWigIterator(fd, verbose, sortedby, scoreType=scoreType)
def wigIterator(fd, verbose=False, sortedby=None, scoreType=int):
# peak at the first line to see if it's a regular wig, or
# fixed-step wig
fh = openFD(fd)
at = fh.tell()
line = None
while (line is None):
l = fh.readline()
if l.strip() != "":
line = l
fh.seek(at)
if line.split()[0] == "fixedStep":
return fixedWigIterator(fd, verbose, sortedby)
else:
return regularWigIterator(fd, verbose, sortedby, scoreType=scoreType)
def fixedWigIterator(fd, verbose=False, sortedby=None, scoreType=int):
"""
@summary:
"""
fh = openFD(fd)
if verbose:
try:
pind = ProgressIndicator(totalToDo=os.path.getsize(fh.name),
messagePrefix="completed",
messageSuffix="of processing " + fh.name)
except AttributeError:
sys.stderr.write("WigIterator -- warning: " +
"unable to show progress for stream")
verbose = False
chromsSeen = set()
prev = None
# NUMBERS = set(['1','2','3','4','5','6','7','8','9','0','.'])
currentChrom, at, step = None, None, None
for line in fh:
line = line.strip()
if line == "":
continue
if line[0] == 't' or line[0] == 'f':
parts = line.split()
if parts[0] == "track":
continue
elif parts[0] == "fixedStep":
currentChrom = parts[1].split("=")[1]
at = int(parts[2].split("=")[1])
step = int(parts[3].split("=")[1])
else:
val = float(line)
e = GenomicInterval(currentChrom,
at,
at + step,
None,
val,
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(
"Wig 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("Wig file " + fd.name +
" not sorted by chrom")
chromsSeen.add(e.chrom)
# all good..
yield e
prev = e
at += step
if verbose:
pind.done = fh.tell()
pind.showProgress()
