Command Line Interface

$ dimspy --help

Executing dimspy version 2.0.0.
usage: __main__.py [-h]
                   {process-scans,replicate-filter,align-samples,blank-filter,sample-filter,remove-samples,mv-sample-filter,merge-peaklists,get-peaklists,get-average-peaklist,hdf5-pm-to-txt,hdf5-pls-to-txt,create-sample-list,unzip,licenses}
                   ...

Python package to process DIMS data

positional arguments:
  {process-scans,replicate-filter,align-samples,blank-filter,sample-filter,remove-samples,mv-sample-filter,merge-peaklists,get-peaklists,get-average-peaklist,hdf5-pm-to-txt,hdf5-pls-to-txt,create-sample-list,unzip,licenses}
    process-scans       Process scans and/or stitch SIM windows.
    replicate-filter    Filter irreproducible peaks from technical replicate
                        peaklists.
    align-samples       Align peaklists across samples.
    blank-filter        Filter peaks across samples that are present in the
                        blank samples.
    sample-filter       Filter peaks based on certain reproducibility and
                        sample class criteria.
    remove-samples      Remove sample(s) from a peak matrix object or list of
                        peaklist objects.
    mv-sample-filter    Filter samples based on the percentage of missing
                        values.
    merge-peaklists     Merge peaklists from multiple lists of peaklist or
                        peak matrix objects.
    get-peaklists       Get peaklists from a peak matrix object.
    get-average-peaklist
                        Get an average peaklist from a peak matrix object.
    hdf5-pm-to-txt      Write HDF5 output (peak matrix) to text format.
    hdf5-pls-to-txt     Write HDF5 output (peak lists) to text format.
    create-sample-list  Create a sample list from a peak matrix object or list
                        of peaklist objects.
    unzip               Extract files from zip file
    licenses            Show licenses DIMSpy and RawFileReader

optional arguments:
  -h, --help            show this help message and exit

$ dimspy process-scans --help

Executing dimspy version 2.0.0b1.
usage: __main__.py process-scans [-h] -i source -o OUTPUT [-l FILELIST] -m
                                 {median,mean,mad,noise_packets} -s
                                 SNR_THRESHOLD [-p PPM] [-n MIN_SCANS]
                                 [-a MIN_FRACTION] [-d RSD_THRESHOLD] [-k]
                                 [-r RINGING_THRESHOLD]
                                 [-e start end scan_type]
                                 [-x start end scan_type] [-z start end]
                                 [-u REPORT] [-b BLOCK_SIZE] [-c NCPUS]

optional arguments:
  -h, --help            show this help message and exit
  -i source, --input source
                        Directory (*.raw, *.mzml or tab-delimited peaklist
                        files), single *.mzml/*.raw file or zip archive
                        (*.mzml only)
  -o OUTPUT, --output OUTPUT
                        HDF5 file to save the peaklist objects to.
  -l FILELIST, --filelist FILELIST
                        Tab-delimited file that include the name of the data
                        files (*.raw or *.mzml) and meta data. Column names:
                        filename, replicate, batch, injectionOrder,
                        classLabel.
  -m {median,mean,mad,noise_packets}, --function-noise {median,mean,mad,noise_packets}
                        Select function to calculate noise.
  -s SNR_THRESHOLD, --snr-threshold SNR_THRESHOLD
                        Signal-to-noise threshold
  -p PPM, --ppm PPM     Mass tolerance in Parts per million to group peaks
                        across scans / mass spectra.
  -n MIN_SCANS, --min_scans MIN_SCANS
                        Minimum number of scans required for each m/z range or
                        event.
  -a MIN_FRACTION, --min-fraction MIN_FRACTION
                        Minimum fraction a peak has to be present. Use 0.0 to
                        not apply this filter.
  -d RSD_THRESHOLD, --rsd-threshold RSD_THRESHOLD
                        Maximum threshold - relative standard deviation
                        (Calculated for peaks that have been measured across a
                        minimum of two scans).
  -k, --skip-stitching  Skip the step where (SIM) windows are 'stitched' or
                        'joined' together. Individual peaklists are generated
                        for each window.
  -r RINGING_THRESHOLD, --ringing-threshold RINGING_THRESHOLD
                        Ringing
  -e start end scan_type, --include-scan-events start end scan_type
                        Scan events to select. E.g. 100.0 200.0 sim or 50.0
                        1000.0 full
  -x start end scan_type, --exclude-scan-events start end scan_type
                        Scan events to select. E.g. 100.0 200.0 sim or 50.0
                        1000.0 full
  -z start end, --remove-mz-range start end
                        M/z range(s) to remove. E.g. 100.0 102.0 or 140.0
                        145.0.
  -u REPORT, --report REPORT
                        Summary/Report of processed mass spectra
  -b BLOCK_SIZE, --block-size BLOCK_SIZE
                        The size of each block of peaks to perform clustering
                        on.
  -c NCPUS, --ncpus NCPUS
                        Number of central processing units (CPUs).