def main():
parser = argparse.ArgumentParser(description="FeatureLinkerUnlabeledQT")
parser.add_argument(
"-in",
action="append",
type=str,
dest="in_",
metavar="input_files",
)
parser.add_argument(
"-out",
action="store",
type=str,
metavar="output_file",
)
parser.add_argument(
"-ini",
action="store",
type=str,
metavar="ini_file",
)
parser.add_argument(
"-dict_ini",
action="store",
type=str,
metavar="python_dict_ini_file",
)
parser.add_argument(
"-write_ini",
action="store",
type=str,
metavar="ini_file",
)
parser.add_argument(
"-write_dict_ini",
action="store",
type=str,
metavar="python_dict_ini_file",
)
parser.add_argument(
"-keep_subelements",
action="store_true",
)
args = parser.parse_args()
def collect(args):
return [f.strip() for arg in args or [] for f in arg.split(",")]
in_files = collect(args.in_)
run_mode = (in_files and args.out) \
and (args.ini is not None or args.dict_ini is not None)
write_mode = args.write_ini is not None or args.write_dict_ini is not None
ok = run_mode or write_mode
if not ok:
parser.error("either specify -in, -out and -(dict)ini for running "
"the feature linker\nor -write(dict)ini for creating std "
"ini file")
defaults = pms.FeatureGroupingAlgorithmQT().getParameters()
write_requested = writeParamsIfRequested(args, defaults)
if not write_requested:
updateDefaults(args, defaults)
link(in_files, args.out, args.keep_subelements, defaults)
def link(in_files, out_file, keep_subelements, params):
in_types = set(pms.FileHandler.getType(in_) for in_ in in_files)
if in_types == set((pms.Type.CONSENSUSXML, )):
link_features = False
elif in_types == set((pms.Type.FEATUREXML, )):
link_features = True
else:
raise Exception("different kinds of input files")
algorithm_parameters = params.copy("algorithm:", True)
algorithm = pms.FeatureGroupingAlgorithmQT()
algorithm.setParameters(algorithm_parameters)
out_map = pms.ConsensusMap()
fds = out_map.getColumnHeaders()
if link_features:
f = pms.FeatureXMLFile()
maps = []
for i, in_file in enumerate(in_files):
map_ = pms.FeatureMap()
f.load(in_file, map_)
# set filedescriptions
fd = fds.get(i, pms.ColumnHeader())
fd.filename = in_file
fd.size = map_.size()
fd.unique_id = map_.getUniqueId()
fds[i] = fd
maps.append(map_)
out_map.setColumnHeaders(fds)
algorithm.group(maps, out_map)
else:
f = pms.ConsensusXMLFile()
maps = []
for i, in_file in enumerate(in_files):
map_ = pms.ConsensusMap()
f.load(in_file, map_)
maps.append(map_)
algorithm.group(maps, out_map)
if not keep_subelements:
for i in range(len(in_files)):
# set filedescriptions
fd = fds.get(i, pms.ColumnHeader())
fd.filename = in_files[i]
fd.size = maps[i].size()
fd.unique_id = maps[i].getUniqueId()
fds[i] = fd
out_map.setColumnHeaders(fds)
else:
algorithm.transferSubelements(maps, out_map)
out_map.setUniqueIds()
addDataProcessing(out_map, params,
pms.DataProcessing.ProcessingAction.FEATURE_GROUPING)
pms.ConsensusXMLFile().store(out_file, out_map)
sizes = []
for feat in out_map:
sizes.append(feat.size())
c = Counter(sizes)
print "Number of consensus features:"
for size, count in c.most_common():
print " of size %2d : %6d" % (size, count)
print " total : %6d" % out_map.size()