Mercurial > repos > galaxyp > openms_metaprosip
view fill_ctd_clargs.py @ 13:819ed5aae76f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 18:58:27 +0000 |
parents | 73c1493ac4c2 |
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#!/usr/bin/env python3 import operator from argparse import ArgumentParser from functools import reduce # forward compatibility for Python 3 from io import StringIO from CTDopts.CTDopts import ( _Null, CTDModel, ModelTypeError, Parameters ) def getFromDict(dataDict, mapList): return reduce(operator.getitem, mapList, dataDict) def setInDict(dataDict, mapList, value): getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value if __name__ == "__main__": # note add_help=False since otherwise arguments starting with -h will # trigger an error (despite allow_abbreviate) parser = ArgumentParser(prog="fill_ctd_clargs", description="fill command line arguments" "into a CTD file and write the CTD file to stdout", add_help=False, allow_abbrev=False) parser.add_argument("--ini_file", dest="ini_file", help="input ini file", metavar='INI', default=None, required=True) parser.add_argument("--ctd_file", dest="ctd_file", help="input ctd file" "if given then optional parameters from the ini file" "will be filled with the defaults from this CTD file", metavar='CTD', default=None, required=False) args, cliargs = parser.parse_known_args() # load CTDModel ini_model = None try: ini_model = CTDModel(from_file=args.ini_file) except ModelTypeError: pass try: ini_model = Parameters(from_file=args.ini_file) except ModelTypeError: pass assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ini_file) # get a dictionary of the ctd arguments where the values of the parameters # given on the command line are overwritten ini_values = ini_model.parse_cl_args(cl_args=cliargs, ignore_required=True) if args.ctd_file: ctd_model = CTDModel(from_file=args.ctd_file) ctd_values = ctd_model.get_defaults() for param in ini_model.get_parameters(): if not param.required and (param.default is None or type(param.default) is _Null): lineage = param.get_lineage(name_only=True) try: default = getFromDict(ctd_values, lineage) except KeyError: continue setInDict(ini_values, lineage, default) # write the ctd with the values taken from the dictionary out = StringIO() ctd_tree = ini_model.write_ctd(out, ini_values) print(out.getvalue())