def getPositions(files):
"""Takes a list of input files and returns
a list of BSPosition's
"""
# func to filter header out
head_filt = lambda line: False if line.startswith("ref") else True
record_it = lambda fh: lineRecordIterator(fh, BSBaseSample, BSBaseSampleTypes, head_filt, "\t")
opener = lambda fn: gzip.open if fn.endswith(".gz") else open
# read all data into a matrix
observations = map(lambda fn: list(fileIterator(fn, record_it, opener(fn))), files)
return map(BSPosition._make, izip(imap(attrgetter("off"), observations[0]), izip(*observations)))
sys.exit(getHelpStr(description, cl_arglist) + "\n")
log = logger(sys.stderr if arg_map["log"] else None)
regionfile = remaining_args[0]
methylfiles = remaining_args[1:]
log("Reading Positions from Files")
positions = getPositions(methylfiles)
pp = PdfPages(arg_map["pout"] + ".pdf")
regmk = lambda arr : Region._make(map(lambda t,v : t(v), RegionTypes, arr[:3]))
regit = lambda fh: iterApply(regmk, lineItemIterator(fh))
for region in fileIterator(regionfile, regit):
if not region.chr == positions[0].samples[0].ref:
raise Exception, "Regions are for a different Chromosome"
log("Working on %s:%d-%d" % region)
def searchexp(item):
if item > region.end:
return -1
elif item < region.start:
return 1
return 0
exp = lambda pos : pos >= region.start and pos <= region.end
fexp = lambda f : lambda p : f(p.pos)
rstart,rend = expandRegion(positions,fexp(exp),
