Command Line InterfaceΒΆ
$ 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).