def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv:
argv = sys.argv
# setup command line parser
parser = E.ArgumentParser(description=__doc__)
parser.add_argument("--version", action='version', version="1.0")
parser.add_argument("-o", "--output-section", dest="output", type=str,
choices=("full", "name"),
help="output either ``full`` overlapping entries, only the ``name``s.")
parser.set_defaults(
output="full",
)
# add common options (-h/--help, ...) and parse command line
(args, unknown) = E.start(parser,
argv=argv,
unknowns=True)
if len(unknown) != 2:
raise ValueError("two arguments required")
if unknown[0] == "-":
infile1 = args.stdin
else:
infile1 = iotools.open_file(unknown[0], "r")
infile2 = iotools.open_file(unknown[1], "r")
idx = Bed.readAndIndex(infile2, with_values=True)
output = args.output
outfile = args.stdout
if output == "name":
outfile.write("name1\tname2\n")
outf = lambda x: x.fields[0]
else:
outf = str
for bed in Bed.iterator(infile1):
try:
overlaps = idx[bed.contig].find(bed.start, bed.end)
except (KeyError, IndexError):
# ignore missing contig and zero length intervals
continue
for o in overlaps:
outfile.write("\t".join((outf(bed), outf(o[2]))) + "\n")
E.stop()
def __init__(self, filename, *args, **kwargs):
assert filename is not None,\
"please supply filename for CounterOverlap"
Counter.__init__(self, *args, **kwargs)
self.filename = filename
E.info("reading intervals from %s" % self.filename)
self.index = Bed.readAndIndex(iotools.open_file(self.filename, "r"),
per_track=True)
E.info("read intervals for %s tracks" % len(self.index))
self.tracks = list(self.index.keys())
self.headers = []
for track in self.tracks:
self.headers.extend(["%s_nover" % track, "%s_bases" % track])
def buildIndex(self, filename):
return Bed.readAndIndex(iotools.open_file(filename, "r"))
def __init__(self, filename):
self.mIndices = Bed.readAndIndex(iotools.open_file(filename, "r"),
per_track=True)
def annotateCpGIslands(infiles, outfile):
'''annotate transcript by absence/presence of CpG islands
'''
cpgfile, tssfile = infiles
cpg = Bed.readAndIndex(iotools.openFile(cpgfile))
extension_upstream = PARAMS["cpg_search_upstream"]
extension_downstream = PARAMS["cpg_search_downstream"]
c = E.Counter()
outf = iotools.openFile(outfile, "w")
outf.write(
"transcript_id\tstrand\tstart\tend\trelative_start\trelative_end\n")
for tss in Bed.iterator(iotools.openFile(tssfile)):
c.tss_total += 1
if tss.strand == "+":
start, end = tss.start - \
extension_upstream, tss.start + extension_downstream
else:
start, end = tss.end - \
extension_downstream, tss.end + extension_upstream
try:
matches = list(cpg[tss.contig].find(start, end))
except KeyError:
c.promotor_without_matches += 1
continue
if len(matches) == 0:
c.promotor_without_matches += 1
continue
c.promotor_output += 1
for match in matches:
c.matches_total += 1
genome_start, genome_end, x = match
l = genome_end - genome_start
# get relative location of match
if tss.strand == "+":
relative_start = genome_start - tss.start
else:
relative_start = tss.end - genome_end
relative_end = relative_start + l
outf.write("\t".join(
map(str, (tss.name, tss.strand, genome_start, genome_end,
relative_start, relative_end))) + "\n")
c.matches_output += 1
outf.close()
with iotools.openFile(outfile + ".summary", "w") as outf:
outf.write("category\tcounts\n")
outf.write(c.asTable() + "\n")
E.info(c)
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(
version=
"%prog version: $Id: bed2graph.py 2861 2010-02-23 17:36:32Z andreas $",
usage=globals()["__doc__"])
parser.add_option(
"-o",
"--output-section",
dest="output",
type="choice",
choices=("full", "name"),
help=
"output either ``full`` overlapping entries, only the ``name``s. [default=%default]."
)
parser.set_defaults(output="full", )
# add common options (-h/--help, ...) and parse command line
(options, args) = E.start(parser, argv=argv)
if len(args) != 2:
raise ValueError("two arguments required")
if args[0] == "-":
infile1 = options.stdin
else:
infile1 = iotools.open_file(args[0], "r")
infile2 = iotools.open_file(args[1], "r")
idx = Bed.readAndIndex(infile2, with_values=True)
output = options.output
outfile = options.stdout
if output == "name":
outfile.write("name1\tname2\n")
outf = lambda x: x.fields[0]
else:
outf = str
for bed in Bed.iterator(infile1):
try:
overlaps = idx[bed.contig].find(bed.start, bed.end)
except (KeyError, IndexError):
# ignore missing contig and zero length intervals
continue
for o in overlaps:
outfile.write("\t".join((outf(bed), outf(o[2]))) + "\n")
E.stop()
