def raw_dir(self, value):
"""
Sets the directory where PerkinElmer or Waters .RAW Files are stored
:param value:
:type value: str or :class:`pathlib.Path`
"""
self._raw_dir = str(relpath2(value))
def log_dir(self, value):
"""
Sets the directory where log files will be stored.
The directory will be created if it does not already exist.
:param value:
:type value: str or :class:`pathlib.Path`
"""
self._log_dir = str(relpath2(value))
maybe_make(self._log_dir)
def msp_dir(self, value):
"""
Sets the directory where MSP files for NIST MS Search will be stored.
The directory will be created if it does not already exist.
:param value:
:type value: str or :class:`pathlib.Path`
"""
self._msp_dir = str(relpath2(value))
maybe_make(self._msp_dir)
def process_path(path):
return str(relpath2(path)).replace("\\", "/")
def save_config(self, configfile=None):
"""
Saves the configuration to the given filename, or to self.configfile if no filename is given
:param configfile: Filename to save the configuration to
:type configfile: str, optional
"""
if configfile is None:
configfile = self.configfile
# Configuration
Config = configparser.ConfigParser()
Config.read(configfile)
if platform.system() == "Linux":
Config.set("main", "LinuxNistPath", self.nist_path)
else:
Config.set("main", "NistPath", self.nist_path.replace("\\", "/"))
Config.set("main", "rawpath",
str(relpath2(self.raw_dir)).replace("\\", "/"))
Config.set("main", "CSVpath",
str(relpath2(self.csv_dir)).replace("\\", "/"))
Config.set("main", "SPECTRApath",
str(relpath2(self.spectra_dir)).replace("\\", "/"))
Config.set("main", "CHARTSpath",
str(relpath2(self.charts_dir)).replace("\\", "/"))
Config.set("main", "MSPpath",
str(relpath2(self.msp_dir)).replace("\\", "/"))
Config.set("main", "RESULTSpath",
str(relpath2(self.results_dir)).replace("\\", "/"))
Config.set("main", "MSPpath",
str(relpath2(self.msp_dir)).replace("\\", "/"))
Config.set("main", "exprdir",
str(relpath2(self.expr_dir)).replace("\\", "/"))
Config.set("samples", "samples", ",".join(self.prefixList))
Config.set("import", "bb_points", str(self.bb_points))
Config.set("import", "bb_scans", str(self.bb_scans))
Config.set("import", "noise_thresh", str(self.noise_thresh))
Config.set("import", "target_range",
"{},{}".format(*self.target_range))
Config.set("import", "exclude_ions", list2str(self.base_peak_filter))
Config.set("import", "tophat", str(self.tophat))
Config.set("import", "tophat_unit", self.tophat_unit)
Config.set("import", "mass_range", "{},{}".format(*self.mass_range))
Config.set("alignment", "rt_modulation", str(self.rt_modulation))
Config.set("alignment", "gap_penalty", str(self.gap_penalty))
Config.set("alignment", "min_peaks", str(self.min_peaks))
Config.set("analysis", "do_quantitative", str(self.do_quantitative))
Config.set("analysis", "do_qualitative", str(self.do_qualitative))
Config.set("analysis", "do_merge", str(self.do_merge))
Config.set("analysis", "do_counter", str(self.do_counter))
Config.set("analysis", "do_spectra", str(self.do_spectra))
Config.set("analysis", "do_charts", str(self.do_charts))
Config.set("comparison", "a", str(self.comparison_a))
Config.set("comparison", "rt_modulation",
str(self.comparison_rt_modulation))
Config.set("comparison", "gap_penalty",
str(self.comparison_gap_penalty))
Config.set("comparison", "min_peaks", str(self.comparison_min_peaks))
with open(configfile, "w") as f:
Config.write(f)