HorIson
HorIson is a tool for vectorized isotope simulation, that applies Fast-fourier transform (FFT) or multinomial products.
How does HorIson work
HorIson provides 3 algorithms for different types of istope simulation.
- FFT_Lowres, which computes convolved coarse isotopes (1 per 1 Da) at high speed.
- FFT_Highres, which computes fine isotopes and profile spectra at variable resolution.
- Multi_conv: which computes separate isotope combinstions at high speed.
To enable vectorization for FFT-based algorithms, isotope masses are placed on a uniform grid. For multinomial products, global isotope combinations and multnomial distribtuions are precomputed.
Usage:
HorIson can be imported as a module, or called from the command line. As input for each algorithm, a failepath to a tabular can be supplied, or an element string, or a DataFrame or array can be used when importing as a module. When no header information is present, the element order should be supplied with the element parameter.
Arguments.
General arguments
| Parameter | Default value | Description |
|---|---|---|
| elements | [] | Specifies element column order if a headerless array is used as input |
| min_itensity | 1e-6 | Filters isotopes in output below a certain probability level |
| isotope_ranges | [-2,6] | Filters isotopes in output to a certain mass range |
| charge | 1 | charge of computed formulas, accepts either single value or array of different charges |
| normalize | False | Normalizes probabilies either total ("sum"), largest isotope ("max") or monoisotopic peak ("mono") |
| batch_size | 1e4 | How many formulas to simulate at once |
| add_mono | True | Add monoisotopic mass back to simluated isotope masses |
| peak_fwhm | 0.01 | Peak FWHM in Da, used for generating profile data (FFT_Highres, Multi_conv), accepts either single value or array of different FWHMs |
| divisor | 4 | Subsampling rate for convolution (FFT_Highres, Multi_conv) |
FFT_Lowres specific arguments
| Parameter | Default value | Description |
|---|---|---|
| bins | False | Set a fixed maximum grid size |
| mass_calc | True | Calculate exact isotope masses |
| return_borders | False | provide grid-sizes as output |
FFT_Highres specific arguments
| Parameter | Default value | Description |
|---|---|---|
| packing | True | Compress redundant grid sections |
| peak_picking | True | Output centroid data |
Mutli_conv specific arguments
| Parameter | Default value | Description |
|---|---|---|
| prune | 1e-6 | remove isotope combinations below a chance threshold or outside of isotope range |
| min_chance | 1e-4 | remove isotope combinations after pruning |
| convolve | "fast" | Output raw combinations (False) or profile (peak) data ("full") or centroid data ("fast") |
| add_borders | False | Compute peak borders |
| add_area | False | Compute peak area |
| Precomputed | [] | Re-use precomputed isotope combinations |
Licensing:
The pipeline is licensed with standard MIT-license.
If you would like to use this pipeline in your research, please cite the following papers:
1 maintainer
Metadata
1 maintainer
Release files for HorIson 0.1.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| horison-0.1.4.tar.gz | 553.8 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| horison-0.1.4-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 1.1 MB
Release files / horison-0.1.4.tar.gz
| Download URL | horison-0.1.4.tar.gz |
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| Size | 553.8 kB |
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| Size | 572.2 kB |
| Tags | Python 3 |
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