MzMLSqliteHandler#
- class pyopenms.MzMLSqliteHandler#
Bases:
object
Cython implementation of _MzMLSqliteHandler
Original C++ documentation is available here
- __init__()#
Overload:
- __init__(self, filename: bytes | str | String, run_id: int) None
Overload:
- __init__(self, in_0: MzMLSqliteHandler) None
Methods
Overload:
createTables
(self)Create data tables for a new file
getNrChromatograms
(self)Returns the number of chromatograms in the file
getNrSpectra
(self)Returns number of spectra in the file, reutrns the number of spectra
getRunID
(self)Extract the RUN ID from the sqMass file
getSpectraIndicesbyRT
(self, RT, deltaRT, indices)Returns spectral indices around a specific retention time
readChromatograms
(self, exp, indices, meta_only)Read a set of chromatograms (potentially restricted to a subset)
readExperiment
(self, exp, meta_only)Read an experiment into an MSExperiment structure
readSpectra
(self, exp, indices, meta_only)Read a set of spectra (potentially restricted to a subset)
setConfig
(self, write_full_meta, ...)Sets file configuration
writeChromatograms
(self, chroms)Writes a set of chromatograms to disk
writeExperiment
(self, exp)Write an MSExperiment to disk
writeRunLevelInformation
(self, exp, ...)Write the run-level information for an experiment into tables
writeSpectra
(self, spectra)Writes a set of spectra to disk
- createTables(self) None #
Create data tables for a new file
- getNrChromatograms(self) int #
Returns the number of chromatograms in the file
- getNrSpectra(self) int #
Returns number of spectra in the file, reutrns the number of spectra
- getRunID(self) int #
Extract the RUN ID from the sqMass file
- getSpectraIndicesbyRT(self, RT: float, deltaRT: float, indices: List[int]) List[int] #
Returns spectral indices around a specific retention time
- Parameters:
RT – The retention time
deltaRT – Tolerance window around RT (if less or equal than zero, only the first spectrum after RT is returned)
indices – Spectra to consider (if empty, all spectra are considered)
- Returns:
The indices of the spectra within RT +/- deltaRT
- readChromatograms(self, exp: List[MSChromatogram], indices: List[int], meta_only: bool) None #
Read a set of chromatograms (potentially restricted to a subset)
- Parameters:
exp – The result data structure
indices – A list of indices restricting the resulting spectra only to those specified here
meta_only – Only read the meta data
- readExperiment(self, exp: MSExperiment, meta_only: bool) None #
Read an experiment into an MSExperiment structure
- Parameters:
exp – The result data structure
meta_only – Only read the meta data
- readSpectra(self, exp: List[MSSpectrum], indices: List[int], meta_only: bool) None #
Read a set of spectra (potentially restricted to a subset)
- Parameters:
exp – The result data structure
indices – A list of indices restricting the resulting spectra only to those specified here
meta_only – Only read the meta data
- setConfig(self, write_full_meta: bool, use_lossy_compression: bool, linear_abs_mass_acc: float) None #
Sets file configuration
- Parameters:
write_full_meta – Whether to write a complete mzML meta data structure into the RUN_EXTRA field (allows complete recovery of the input file)
use_lossy_compression – Whether to use lossy compression (ms numpress)
linear_abs_mass_acc – Accepted loss in mass accuracy (absolute m/z, in Th)
- writeChromatograms(self, chroms: List[MSChromatogram]) None #
Writes a set of chromatograms to disk
- writeExperiment(self, exp: MSExperiment) None #
Write an MSExperiment to disk
- writeRunLevelInformation(self, exp: MSExperiment, write_full_meta: bool) None #
Write the run-level information for an experiment into tables
This is a low level function, do not call this function unless you know what you are doing
- Parameters:
exp – The result data structure
meta_only – Only read the meta data
- writeSpectra(self, spectra: List[MSSpectrum]) None #
Writes a set of spectra to disk