def id_mapper(in_file, id_file, out_file, params, use_centroid_rt,
use_centroid_mz, use_subelements):
in_type = pms.FileHandler.getType(in_file)
protein_ids = []
peptide_ids = []
pms.IdXMLFile().load(id_file, protein_ids, peptide_ids)
mapper = pms.IDMapper()
mapper.setParameters(params)
if in_type == pms.Type.CONSENSUSXML:
file_ = pms.ConsensusXMLFile()
map_ = pms.ConsensusMap()
file_.load(in_file, map_)
mapper.annotate(map_, peptide_ids, protein_ids, use_subelements)
addDataProcessing(
map_, params,
pms.DataProcessing.ProcessingAction.IDENTIFICATION_MAPPING)
file_.store(out_file, map_)
elif in_type == pms.Type.FEATUREXML:
file_ = pms.FeatureXMLFile()
map_ = pms.FeatureMap()
file_.load(in_file, map_)
mapper.annotate(map_, peptide_ids, protein_ids, use_centroid_rt,
use_centroid_mz)
addDataProcessing(
map_, params,
pms.DataProcessing.ProcessingAction.IDENTIFICATION_MAPPING)
file_.store(out_file, map_)
elif in_type == pms.Type.MZQ:
file_ = pms.MzQuantMLFile()
msq = pms.MSQuantifications()
file_.load(in_file, msq)
maps = msq.getConsensusMaps()
for map_ in maps:
mapper.annotate(map_, peptide_ids, protein_ids, use_subelements)
addDataProcessing(
map_, params,
pms.DataProcessing.ProcessingAction.IDENTIFICATION_MAPPING)
msq.setConsensusMaps(maps)
file_.store(out_file, msq)
else:
raise Exception("invalid input file format")
def main():
parser = argparse.ArgumentParser(description="IDMapper")
parser.add_argument(
"-id",
action="store",
type=str,
dest="id_",
metavar="id_file",
)
parser.add_argument(
"-in",
action="store",
type=str,
dest="in_",
metavar="input_file",
)
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("-mz_tolerance", action="store", type=float)
parser.add_argument("-rt_tolerance", action="store", type=float)
parser.add_argument("-mz_measure", action="store", type=str)
parser.add_argument("-mz_reference", action="store", type=str)
parser.add_argument("-ignore_charge", action="store_true")
parser.add_argument("-feature:use_centroid_rt", action="store_true")
parser.add_argument("-feature:use_centroid_mz", action="store_true")
parser.add_argument("-consensusfeature:use_subelements",
action="store_true")
args = parser.parse_args()
run_mode = (args.in_ and args.id_ 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 -id, -in, -out and -(dict)ini for running "
"the id mapper\nor -write(dict)ini for creating std "
"ini file")
defaults = pms.IDMapper().getParameters()
write_requested = writeParamsIfRequested(args, defaults)
if not write_requested:
updateDefaults(args, defaults)
dd = defaults.asDict()
dd["ignore_charge"] = "true" if args.ignore_charge else "false"
for att in [
"mz_tolerance", "rt_tolerance", "mz_measure", "mz_reference"
]:
value = getattr(args, att)
if value is not None:
dd[att] = value
defaults.update(dd)
feature_use_centroid_rt = getattr(args, "feature:use_centroid_rt")
feature_use_centroid_mz = getattr(args, "feature:use_centroid_mz")
consenususfeature_use_subelements = getattr(
args, "consensusfeature:use_subelements")
id_mapper(args.in_, args.id_, args.out, defaults,
feature_use_centroid_rt, feature_use_centroid_mz,
consenususfeature_use_subelements)