MzMLFile#
- class pyopenms.MzMLFile#
Bases:
object
Cython implementation of _MzMLFile
- Original C++ documentation is available here
– Inherits from [‘ProgressLogger’]
File adapter for MzML files
Provides methods to load and store MzML files. PeakFileOptions allow to load a reduced subset of the data into an MSExperiment.
See help(MSExperiment) how data is stored after loading. See help(PeakFileOptions) for available options.
Usage:
exp = MSExperiment() MzMLFile().load("test.mzML", exp) spec = [] for s in exp.getSpectra(): if s.getMSLevel() != 1: spec.append(s) exp.setSpectra(spec) MzMLFile().store("filtered.mzML", exp)
Methods
Overload:
endProgress
(self)Ends the progress display
getLogType
(self)Returns the type of progress log being used
getOptions
(self)isSemanticallyValid
(self, filename, errors, ...)load
(self, filename, in_1)Loads from an MzML file.
loadBuffer
(self, input, exp)Loads a map from a MzML file stored in a buffer (in memory)
nextProgress
(self)Increment progress by 1 (according to range begin-end)
setLogType
(self, in_0)Sets the progress log that should be used.
setOptions
(self, in_0)Set PeakFileOptions to perform filtering during loading.
setProgress
(self, value)Sets the current progress
startProgress
(self, begin, end, label)store
(self, filename, in_1)Stores a MSExperiment in an MzML file
storeBuffer
(self, output, exp)Stores a map in an output string
- endProgress(self) None #
Ends the progress display
- getLogType(self) int #
Returns the type of progress log being used
- getOptions(self) PeakFileOptions #
- isSemanticallyValid(self, filename: bytes | str | String, errors: List[bytes], warnings: List[bytes]) bool #
- load(self, filename: bytes | str | String, in_1: MSExperiment) None #
Loads from an MzML file. Spectra and chromatograms are sorted by default (this can be disabled using PeakFileOptions)
- loadBuffer(self, input: bytes | str | String, exp: MSExperiment) None #
Loads a map from a MzML file stored in a buffer (in memory)
- Parameters:
buffer – The buffer with the data (i.e. string with content of an mzML file)
exp – Is an MSExperiment
- Raises:
Exception: ParseError is thrown if an error occurs during parsing
- nextProgress(self) None #
Increment progress by 1 (according to range begin-end)
- setLogType(self, in_0: int) None #
Sets the progress log that should be used. The default type is NONE!
- setOptions(self, in_0: PeakFileOptions) None #
Set PeakFileOptions to perform filtering during loading. E.g., to load only MS1 spectra or meta data only
- setProgress(self, value: int) None #
Sets the current progress
- store(self, filename: bytes | str | String, in_1: MSExperiment) None #
Stores a MSExperiment in an MzML file
- storeBuffer(self, output: String, exp: MSExperiment) None #
Stores a map in an output string
- Parameters:
output – An empty string to store the result
exp – Has to be an MSExperiment
- transform()#