FileHandler

class pyopenms.FileHandler().loadExperiment("test.mzML", exp)

Bases: object

__init__(self) → None

Attributes

computeFileHash
getConsistentOutputfileType
getFeatOptions	Returns a copy of the feature file options for loading/storing
getOptions	Access to the options for loading/storing
getType
getTypeByContent
getTypeByFileName
hasValidExtension
isSupported
loadConsensusFeatures	Overloaded function.
loadExperiment	Overloaded function.
loadFeatures	Overloaded function.
loadIdentifications	Overloaded function.
loadSpectrum	Overloaded function.
loadTransformations	Overloaded function.
loadTransitions	Overloaded function.
setFeatOptions	Set feature file options for loading/storing
setOptions	Sets options for loading/storing
storeConsensusFeatures	Overloaded function.
storeExperiment	Overloaded function.
storeFeatures	Overloaded function.
storeIdentifications	Overloaded function.
storeSpectrum	Overloaded function.
storeTransformations	Overloaded function.
storeTransitions	Overloaded function.
stripExtension
swapExtension

computeFileHash = <nanobind.nb_func object>

getConsistentOutputfileType = <nanobind.nb_func object>

getFeatOptions

Returns a copy of the feature file options for loading/storing

getOptions

Access to the options for loading/storing

getType = <nanobind.nb_func object>

getTypeByContent = <nanobind.nb_func object>

getTypeByFileName = <nanobind.nb_func object>

hasValidExtension = <nanobind.nb_func object>

isSupported = <nanobind.nb_func object>

loadConsensusFeatures

Overloaded function.

1. loadConsensusFeatures(self, filename: str) -> pyopenms._pyopenms_kernel.ConsensusMap

Load a ConsensusMap from a file

2. loadConsensusFeatures(self, filename: str, allowed_types: collections.abc.Sequence[pyopenms._pyopenms_format.FileTypes.FileType], log: pyopenms._pyopenms_misc.ProgressLogger.LogType) -> pyopenms._pyopenms_kernel.ConsensusMap

Load a ConsensusMap from a file with options

loadExperiment

Overloaded function.

1. loadExperiment(self, filename: str, exp: pyopenms._pyopenms_experiment.MSExperiment) -> None

Load experiment from file. Thermo .raw files are centroided with Thermo’s peak picking; use ThermoRawFile to keep the scans as acquired

2. loadExperiment(self, filename: str, exp: pyopenms._pyopenms_experiment.MSExperiment, allowed_types: collections.abc.Sequence[pyopenms._pyopenms_format.FileTypes.FileType], log: pyopenms._pyopenms_misc.ProgressLogger.LogType, rewrite_source_file: bool = False, compute_hash: bool = False) -> None

Load experiment with options

loadFeatures

Overloaded function.

1. loadFeatures(self, filename: str) -> pyopenms._pyopenms_kernel.FeatureMap

Loads features from a file into a FeatureMap (auto-detect file type) :param filename: The name of the file to load features from :returns: FeatureMap containing the loaded features :raises: Exception: FileNotFound is thrown if the file could not be opened

2. loadFeatures(self, filename: str, allowed_types: collections.abc.Sequence[pyopenms._pyopenms_format.FileTypes.FileType], log: pyopenms._pyopenms_misc.ProgressLogger.LogType) -> pyopenms._pyopenms_kernel.FeatureMap

Loads features from a file into a FeatureMap :param filename: The name of the file to load features from :param allowed_types: List of allowed file types :param log: Progress logging mode :returns: FeatureMap containing the loaded features :raises: Exception: FileNotFound is thrown if the file could not be opened

loadIdentifications

Overloaded function.

1. loadIdentifications(self, filename: str) -> tuple

Load identifications from file. Returns (list[ProteinIdentification], PeptideIdentificationList)

2. loadIdentifications(self, filename: str, allowed_types: collections.abc.Sequence[pyopenms._pyopenms_format.FileTypes.FileType], log: pyopenms._pyopenms_misc.ProgressLogger.LogType) -> tuple

Load identifications from file with options. Returns (list[ProteinIdentification], PeptideIdentificationList)

loadSpectrum

Overloaded function.

1. loadSpectrum(self, filename: str) -> pyopenms._pyopenms_spectrum.MSSpectrum

Load a single MSSpectrum from a file

2. loadSpectrum(self, filename: str, allowed_types: collections.abc.Sequence[pyopenms._pyopenms_format.FileTypes.FileType]) -> pyopenms._pyopenms_spectrum.MSSpectrum

Load a single MSSpectrum from a file with allowed types filter

loadTransformations

Overloaded function.

1. loadTransformations(self, filename: str, fit_model: bool = True) -> pyopenms._pyopenms_analysis.TransformationDescription

Load transformation description from file

2. loadTransformations(self, filename: str, fit_model: bool, allowed_types: collections.abc.Sequence[pyopenms._pyopenms_format.FileTypes.FileType]) -> pyopenms._pyopenms_analysis.TransformationDescription

Load transformation description from file with allowed types filter

loadTransitions

Overloaded function.

1. loadTransitions(self, filename: str) -> pyopenms._pyopenms_analysis.TargetedExperiment

Load targeted experiment transitions from file

2. loadTransitions(self, filename: str, allowed_types: collections.abc.Sequence[pyopenms._pyopenms_format.FileTypes.FileType], log: pyopenms._pyopenms_misc.ProgressLogger.LogType) -> pyopenms._pyopenms_analysis.TargetedExperiment

Load targeted experiment transitions from file with options

setFeatOptions

Set feature file options for loading/storing

setOptions

Sets options for loading/storing

storeConsensusFeatures

Overloaded function.

1. storeConsensusFeatures(self, filename: str, map: pyopenms._pyopenms_kernel.ConsensusMap) -> None

Store a ConsensusMap to a file

2. storeConsensusFeatures(self, filename: str, map: pyopenms._pyopenms_kernel.ConsensusMap, allowed_types: collections.abc.Sequence[pyopenms._pyopenms_format.FileTypes.FileType], log: pyopenms._pyopenms_misc.ProgressLogger.LogType) -> None

Store a ConsensusMap to a file with options

storeExperiment

Overloaded function.

1. storeExperiment(self, filename: str, exp: pyopenms._pyopenms_experiment.MSExperiment) -> None

Store experiment to file

2. storeExperiment(self, filename: str, exp: pyopenms._pyopenms_experiment.MSExperiment, allowed_types: collections.abc.Sequence[pyopenms._pyopenms_format.FileTypes.FileType], log: pyopenms._pyopenms_misc.ProgressLogger.LogType) -> None

Store experiment with options

storeFeatures

Overloaded function.

1. storeFeatures(self, filename: str, map: pyopenms._pyopenms_kernel.FeatureMap) -> None

Store a FeatureMap to a file

2. storeFeatures(self, filename: str, map: pyopenms._pyopenms_kernel.FeatureMap, allowed_types: collections.abc.Sequence[pyopenms._pyopenms_format.FileTypes.FileType], log: pyopenms._pyopenms_misc.ProgressLogger.LogType) -> None

Store a FeatureMap to a file with options

storeIdentifications

Overloaded function.

1. storeIdentifications(self, filename: str, proteins: collections.abc.Sequence[pyopenms._pyopenms_kernel.ProteinIdentification], peptides: pyopenms._pyopenms_metadata.PeptideIdentificationList) -> None

Store identifications to file

2. storeIdentifications(self, filename: str, proteins: collections.abc.Sequence[pyopenms._pyopenms_kernel.ProteinIdentification], peptides: pyopenms._pyopenms_metadata.PeptideIdentificationList, allowed_types: collections.abc.Sequence[pyopenms._pyopenms_format.FileTypes.FileType], log: pyopenms._pyopenms_misc.ProgressLogger.LogType) -> None

Store identifications to file with options

storeSpectrum

Overloaded function.

1. storeSpectrum(self, filename: str, spec: pyopenms._pyopenms_spectrum.MSSpectrum) -> None

Store a single MSSpectrum to a file

2. storeSpectrum(self, filename: str, spec: pyopenms._pyopenms_spectrum.MSSpectrum, allowed_types: collections.abc.Sequence[pyopenms._pyopenms_format.FileTypes.FileType]) -> None

Store a single MSSpectrum to a file with allowed types filter

storeTransformations

Overloaded function.

1. storeTransformations(self, filename: str, map: pyopenms._pyopenms_analysis.TransformationDescription) -> None

Store transformation description to file

2. storeTransformations(self, filename: str, map: pyopenms._pyopenms_analysis.TransformationDescription, allowed_types: collections.abc.Sequence[pyopenms._pyopenms_format.FileTypes.FileType]) -> None

Store transformation description to file with allowed types filter

storeTransitions

Overloaded function.

1. storeTransitions(self, filename: str, library: pyopenms._pyopenms_analysis.TargetedExperiment) -> None

Store targeted experiment transitions to file

2. storeTransitions(self, filename: str, library: pyopenms._pyopenms_analysis.TargetedExperiment, allowed_types: collections.abc.Sequence[pyopenms._pyopenms_format.FileTypes.FileType], log: pyopenms._pyopenms_misc.ProgressLogger.LogType) -> None

Store targeted experiment transitions to file with options

stripExtension = <nanobind.nb_func object>

swapExtension = <nanobind.nb_func object>