OpenMS
OpenSwathMzMLFileCacher

Serialize a spectra and/or chromatogram mzML file

This class will serialize a spectra and/or chromatogram mzML file and store it in a binary format that contains ONLY the spectra and chromatogram data (no metadata).

This is implemented using the write_memdump and read_memdump functions. For reading there are 2 options

  • read the whole file into the OpenMS datastructures
  • read only an index (read_memdump_idx) of the spectra and chromatograms and then use random-access to retrieve a specific spectra from the disk (read_memdump_spectra)
Note
This tool is experimental!

The command line parameters of this tool are:

OpenSwathMzMLFileCacher -- Caches the spectra and chromatogram data of an mzML to disk.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenSwathMzMLFileCacher.html
Version: 3.2.0-pre-nightly-2024-07-21 Jul 22 2024, 02:13:52, Revision: b650df0
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  OpenSwathMzMLFileCacher <options>

Options (mandatory options marked with '*'):
  -in <file>*                Input mzML file (valid formats: 'mzML', 'sqMass')
  -in_type <type>            Input file type -- default: determined from file extension or content
                              (valid: 'mzML', 'sqMass')
  -out <file>*               Output file (valid formats: 'mzML', 'sqMass')
  -out_type <type>           Output file type -- default: determined from file extension or content
                             Note: that not all conversion paths work or make sense. (valid: 'mzML', 'sqMass'
                             )
  -convert_back              Convert back to mzML
  -lossy_compression <type>  Use numpress compression to achieve optimally small file size (attention: may 
                             cause small loss of precision; only for mzML data). (default: 'true') (valid: 
                             'true', 'false')
  -full_meta <type>          Write full meta information into sqMass file (may require large amounts of memor
                             y) (default: 'true') (valid: 'true', 'false')
                             
Common TOPP options:
  -ini <file>                Use the given TOPP INI file
  -threads <n>               Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>          Writes the default configuration file
  --help                     Shows options
  --helphelp                 Shows all options (including advanced)

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+OpenSwathMzMLFileCacherCaches the spectra and chromatogram data of an mzML to disk.
version3.2.0-pre-nightly-2024-07-21 Version of the tool that generated this parameters file.
++1Instance '1' section for 'OpenSwathMzMLFileCacher'
in Input mzML fileinput file*.mzML, *.sqMass
in_type input file type -- default: determined from file extension or content
mzML, sqMass
out Output fileoutput file*.mzML, *.sqMass
out_type Output file type -- default: determined from file extension or content
Note: that not all conversion paths work or make sense.
mzML, sqMass
convert_backfalse Convert back to mzMLtrue, false
lossy_compressiontrue Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data).true, false
full_metatrue Write full meta information into sqMass file (may require large amounts of memory)true, false
lossy_mass_accuracy-1.0 Desired (absolute) m/z accuracy for lossy compression (e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy).
process_lowmemoryfalse Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML).
Note: this flag will prevent conversion from spectra to chromatograms.
true, false
lowmem_batchsize500 The batch size of the low memory conversion0:∞
log Name of log file (created only when specified)
debug0 Sets the debug level
threads1 Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse Disables progress logging to command linetrue, false
forcefalse Overrides tool-specific checkstrue, false
testfalse Enables the test mode (needed for internal use only)true, false