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)

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: MzMLFile) → None

Methods

`__init__`	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
`transform`

endProgress(self) → None: Ends the progress display

getLogType(self) → int: Returns the type of progress log being used

getOptions(self) → PeakFileOptions

isSemanticallyValid(self, filename: Union[bytes, str, String], errors: List[bytes], warnings: List[bytes]) → bool

load(self, filename: Union[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: Union[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

startProgress(self, begin: int, end: int, label: Union[bytes, str, String]) → None

store(self, filename: Union[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()