def test_index_genome_alig(self, mock_open):
"""Do a full round trip test for a simple whole-genome alignment."""
in_strm = StringIO.StringIO(self.ga_maf1)
idx_strm = StringIO.StringIO()
# replace open with mock
def open_side_effect(*args, **kwargs):
if not isinstance(args[0], basestring):
raise TypeError()
if args[0] == "one.maf":
return in_strm
elif args[0] == "one.idx":
return idx_strm
raise IOError("No such file")
mock_open.side_effect = open_side_effect
main(["build", "-o", "one.idx", "one.maf"])
idx_strm.seek(0)
in_strm.seek(0)
ga = build_genome_alignment_from_file("one.maf", "hg19", "one.idx")
b1_res = ga.get_blocks("chr22", 1711, 1720)[0]
b2_res = ga.get_blocks("chr22", 1770, 1780)[0]
self.assertEqual(b1_res["hg19.chr22"], self.b1_hg19)
self.assertEqual(b2_res["hg19.chr22"], self.b2_hg19)
def test_index_genome_alig(self, mock_open):
"""Do a full round trip test for a simple whole-genome alignment."""
in_strm = StringIO.StringIO(self.ga_maf1)
idx_strm = StringIO.StringIO()
# replace open with mock
def open_side_effect(*args, **kwargs):
if not isinstance(args[0], basestring):
raise TypeError()
if args[0] == "one.maf":
return in_strm
elif args[0] == "one.idx":
return idx_strm
raise IOError("No such file")
mock_open.side_effect = open_side_effect
main(["build", "-o", "one.idx", "one.maf"])
idx_strm.seek(0)
in_strm.seek(0)
ga = build_genome_alignment_from_file("one.maf", "hg19", "one.idx")
b1_res = ga.get_blocks("chr22", 1711, 1720)[0]
b2_res = ga.get_blocks("chr22", 1770, 1780)[0]
self.assertEqual(b1_res["hg19.chr22"], self.b1_hg19)
self.assertEqual(b2_res["hg19.chr22"], self.b2_hg19)
def main(args, prog_name):
"""Process the command line arguments of this script and dispatch."""
# get options and arguments
ui = getUI(prog_name, args)
if ui.optionIsSet("test"):
# just run unit tests
unittest.main(argv=[sys.argv[0]])
elif ui.optionIsSet("help"):
# just show help
ui.usage()
else:
verbose = (ui.optionIsSet("verbose") is True) or DEFAULT_VERBOSITY
# get output handle
out_fh = sys.stdout
if ui.optionIsSet("output"):
out_fh = open(ui.getValue("output"), "w")
# get window size...
window_size = DEFAULT_WINDOW_SIZE
if ui.optionIsSet("window"):
window_size = ui.getValue("window")
# get the window anchoring location
windowCentre = DEFAULT_WINDOW_CENTRE
if ui.optionIsSet("centre"):
windowCentre = ui.getValue("centre")
if windowCentre not in WINDOW_CENTRE_OPTIONS:
sys.stderr.write("un-recognised window anchor position: " +
str(windowCentre) + "\n")
sys.exit(1)
args = ui.getAllArguments()
assert(len(args) == 3 or len(args) == 4)
region_fn = ui.getArgument(0)
ga_path = ui.getArgument(1)
index_fn = None
if len(args) == 3:
spec = ui.getArgument(2)
else:
index_fn = ui.getArgument(2)
spec = ui.getArgument(3)
extensions = (ui.getValue("extensions").strip().split(",") if
ui.optionIsSet("extensions") else None)
index_extensions = (ui.getValue("index-extensions").strip().split(",") if
ui.optionIsSet("index-extensions") else None)
fail_no_index = ui.optionIsSet("fail-no-index")
mi_seqs = (MissingSequenceHandler[ui.getValue("missing")]
if ui.optionIsSet("missing")
else MissingSequenceHandler.TREAT_AS_ALL_GAPS)
species = ([x.strip() for x in ui.getValue("species").split(",")] if
ui.optionIsSet("species") else None)
# build the genome alignment
alig = (load_just_in_time_genome_alignment(ga_path, spec, extensions,
index_extensions, fail_no_index,
verbose)
if os.path.isdir(ga_path)
else build_genome_alignment_from_file(ga_path, spec, index_fn,
verbose))
# get the profile and write it to the output stream
profile = processBED(open(region_fn), alig, window_size, CENTRE,
mi_seqs, species, verbose)
out_fh.write("\n\n" + ", ".join(str(x) for x in profile) + "\n")
def main(args, prog_name):
"""Process the command line arguments of this script and dispatch."""
# get options and arguments
ui = getUI(prog_name, args)
if ui.optionIsSet("test"):
# just run unit tests
unittest.main(argv=[sys.argv[0]])
elif ui.optionIsSet("help"):
# just show help
ui.usage()
else:
verbose = (ui.optionIsSet("verbose") is True) or DEFAULT_VERBOSITY
# get output handle
out_fh = sys.stdout
if ui.optionIsSet("output"):
out_fh = open(ui.getValue("output"), "w")
# get window size...
window_size = DEFAULT_WINDOW_SIZE
if ui.optionIsSet("window"):
window_size = ui.getValue("window")
# get the window anchoring location
windowCentre = DEFAULT_WINDOW_CENTRE
if ui.optionIsSet("centre"):
windowCentre = ui.getValue("centre")
if windowCentre not in WINDOW_CENTRE_OPTIONS:
sys.stderr.write("un-recognised window anchor position: " +
str(windowCentre) + "\n")
sys.exit(1)
args = ui.getAllArguments()
assert (len(args) == 3 or len(args) == 4)
region_fn = ui.getArgument(0)
ga_path = ui.getArgument(1)
index_fn = None
if len(args) == 3:
spec = ui.getArgument(2)
else:
index_fn = ui.getArgument(2)
spec = ui.getArgument(3)
extensions = (ui.getValue("extensions").strip().split(",")
if ui.optionIsSet("extensions") else None)
index_extensions = (ui.getValue("index-extensions").strip().split(",")
if ui.optionIsSet("index-extensions") else None)
fail_no_index = ui.optionIsSet("fail-no-index")
mi_seqs = (MissingSequenceHandler[ui.getValue("missing")]
if ui.optionIsSet("missing") else
MissingSequenceHandler.TREAT_AS_ALL_GAPS)
species = ([x.strip() for x in ui.getValue("species").split(",")]
if ui.optionIsSet("species") else None)
# build the genome alignment
alig = (load_just_in_time_genome_alignment(
ga_path, spec, extensions, index_extensions, fail_no_index,
verbose) if
os.path.isdir(ga_path) else build_genome_alignment_from_file(
ga_path, spec, index_fn, verbose))
# get the profile and write it to the output stream
profile = processBED(open(region_fn), alig, window_size, CENTRE,
mi_seqs, species, verbose)
out_fh.write("\n\n" + ", ".join(str(x) for x in profile) + "\n")