def main():
parser = argparse.ArgumentParser(description="PeakPickerHiRes")
parser.add_argument("-in",
action="append",
type=str,
dest="in_",
metavar="input_file",
)
parser.add_argument("-seeds",
action="store",
type=str,
metavar="seeds_file",
)
parser.add_argument("-out",
action="append",
type=str,
metavar="output_file",
)
parser.add_argument("-trafo_out",
action="append",
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("-reference:file",
action="store",
type=str,
metavar="reference_file",
dest="reference_file",
)
parser.add_argument("-reference:index",
action="store",
type=int,
metavar="reference_index",
dest="reference_index",
)
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_)
out_files = collect(args.out)
trafo_out_files = collect(args.trafo_out)
run_mode = (in_files and (out_files or trafo_out_files))\
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, -(trafo_)out and -(dict)ini for running "
"the map aligner\nor -write(dict)ini for creating std "
"ini file")
defaults = getDefaultParameters()
write_requested = writeParamsIfRequested(args, defaults)
if not write_requested:
updateDefaults(args, defaults)
if not out_files and not trafo_out_files:
parser.error("need -out or -trafo_out files")
if out_files and len(out_files) != len(in_files):
parser.error("need as many -out files as -in files")
if trafo_out_files and len(trafo_out_files) != len(in_files):
parser.error("need as many -trafo_out files as -in files")
if args.reference_index is not None and args.reference_file is not None:
parser.error("can only handle either reference:index or reference:file")
if args.reference_index is not None:
if args.reference_index <0 or args.reference_index >= len(in_files):
parser.error("reference:index invalid")
if args.reference_file is not None:
if args.reference_file not in in_files:
parser.error("reference_file not in input files")
align(in_files, out_files, trafo_out_files, args.reference_index or 0,
args.reference_file or "", defaults)
def main():
parser = argparse.ArgumentParser(description="PeakPickerHiRes")
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",
)
args = parser.parse_args()
run_mode = args.in_ is not None and args.out is not None\
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 peakpicker\nor -write(dict)ini for creating std "
"ini file")
defaults = pms.PeakPickerHiRes().getDefaults()
write_requested = writeParamsIfRequested(args, defaults)
if not write_requested:
updateDefaults(args, defaults)
fh = pms.MzMLFile()
fh.setLogType(pms.LogType.CMD)
input_map = pms.MSExperiment()
fh.load(args.in_, input_map)
run_peak_picker(input_map, defaults, args.out)
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)
def main():
parser = argparse.ArgumentParser(description="PeakPickerHiRes")
parser.add_argument(
"-in",
action="append",
type=str,
dest="in_",
metavar="input_file",
)
parser.add_argument(
"-seeds",
action="store",
type=str,
metavar="seeds_file",
)
parser.add_argument(
"-out",
action="append",
type=str,
metavar="output_file",
)
parser.add_argument(
"-trafo_out",
action="append",
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(
"-reference:file",
action="store",
type=str,
metavar="reference_file",
dest="reference_file",
)
parser.add_argument(
"-reference:index",
action="store",
type=int,
metavar="reference_index",
dest="reference_index",
)
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_)
out_files = collect(args.out)
trafo_out_files = collect(args.trafo_out)
run_mode = (in_files and (out_files or trafo_out_files))\
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, -(trafo_)out and -(dict)ini for running "
"the map aligner\nor -write(dict)ini for creating std "
"ini file")
defaults = getDefaultParameters()
write_requested = writeParamsIfRequested(args, defaults)
if not write_requested:
updateDefaults(args, defaults)
if not out_files and not trafo_out_files:
parser.error("need -out or -trafo_out files")
if out_files and len(out_files) != len(in_files):
parser.error("need as many -out files as -in files")
if trafo_out_files and len(trafo_out_files) != len(in_files):
parser.error("need as many -trafo_out files as -in files")
if args.reference_index is not None and args.reference_file is not None:
parser.error(
"can only handle either reference:index or reference:file")
if args.reference_index is not None:
if args.reference_index < 0 or args.reference_index >= len(
in_files):
parser.error("reference:index invalid")
if args.reference_file is not None:
if args.reference_file not in in_files:
parser.error("reference_file not in input files")
align(in_files, out_files, trafo_out_files, args.reference_index or 0,
args.reference_file or "", defaults)
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 main():
parser = argparse.ArgumentParser(description="PeakPickerHiRes")
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",
)
args = parser.parse_args()
run_mode = args.in_ is not None and args.out is not None\
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 peakpicker\nor -write(dict)ini for creating std "
"ini file")
defaults = pms.PeakPickerHiRes().getDefaults()
write_requested = writeParamsIfRequested(args, defaults)
if not write_requested:
updateDefaults(args, defaults)
fh = pms.MzMLFile()
fh.setLogType(pms.LogType.CMD)
input_map = pms.MSExperiment()
fh.load(args.in_, input_map)
run_peak_picker(input_map, defaults, args.out)
def main():
parser = argparse.ArgumentParser(description="FeatureFinderCentroided")
parser.add_argument("-in",
action="store",
type=str,
dest="in_",
metavar="input_file",
)
parser.add_argument("-seeds",
action="store",
type=str,
metavar="seeds_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",
)
args = parser.parse_args()
run_mode = args.in_ is not None and args.out is not None\
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 peakpicker\nor -write(dict)ini for creating std "
"ini file")
name = pms.FeatureFinderAlgorithmPicked.getProductName()
defaults = pms.FeatureFinder().getParameters(name)
write_requested = writeParamsIfRequested(args, defaults)
if not write_requested:
updateDefaults(args, defaults)
seeds = pms.FeatureMap()
if args.seeds:
fh = pms.FeatureXMLFile()
fh.load(args.seeds, seeds)
run_featurefinder_centroided(args.in_, defaults, seeds, args.out)
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
)
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)