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pymsConvert

Convert between common MS data formats.

pymsConvert is build on top of pyopenms. Custom implementations of file I\O functions not available in pyopenms, including MS2File.store() are included. pymsConvert is also written to manage and process multiple files in parallel.

Supported formats

  • mzXML
  • mzML
  • ms2

Usage

usage: main.py [-h] -i {mzXML,mzML,ms2,ms1,mgf} -o {mzXML,mzML,ms2,ms1,mgf}
               [--nThread NTHREAD] [--ofname OFNAME]
               input_file [input_file ...]

Convert between various ms data formats.

positional arguments:
  input_file

optional arguments:
  -h, --help            show this help message and exit
  -i {mzXML,mzML,ms2,ms1,mgf}, --inType {mzXML,mzML,ms2,ms1,mgf}
                        Input file type.
  -o {mzXML,mzML,ms2,ms1,mgf}, --outType {mzXML,mzML,ms2,ms1,mgf}
                        Output file type
  --nThread NTHREAD     Specify number of threads to use. By default, each
                        file is processed in its own thread, up to the number
                        of supported threads on the system.
  --ofname OFNAME       Output file name. Default is input file base name with
                        outType extension.