nplinker
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NPLinker
A python framework for data mining microbial natural products by integrating genomics and metabolomics data
Update releasing workflow in `README.dev.md` - update version - create Github release - publish to Pypi
Dependency issue when running `install-nplinker-deps`: ``` ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following...
To be consistent with the `run_bigscape` function that can handle both bigscape versions, it would be nice to merge the [BigscapeV2GCFLoader](https://github.com/NPLinker/nplinker/blob/f767bfad74bc3c5e688864349c78060b4727c4d8/src/nplinker/genomics/bigscape/bigscape_loader.py#L64C7-L64C26) into [BigscapeGCFLoader](https://github.com/NPLinker/nplinker/blob/f767bfad74bc3c5e688864349c78060b4727c4d8/src/nplinker/genomics/bigscape/bigscape_loader.py#L13) and use bigscape version as an argument...
Bigscape version has been introduced to the config file in #251. It's ready to update the [logics](https://github.com/NPLinker/nplinker/blob/f767bfad74bc3c5e688864349c78060b4727c4d8/src/nplinker/loader.py#L216) in `DatasetLoader` to use bigscape version to decide what file to load.
Besides using nplinker in [python environment](https://nplinker.github.io/nplinker/latest/quickstart/#4-run-nplinker), users may also like using command lines for nplinker. This feature request is originally from Artem. Some example commands users might desire: ``` npl...
Problem: the `GNPSFileMappingLoader._load_mapping_fbmn` overwrites the existing mapping for duplicated row ID. Example file: `tests/data/nodes_fbmn.csv` file, row ID 1955 and 1957 are duplicated. ```[tasklist] ### Tasks - [ ] Should the...
Add the option to parse a user-supplied list of strain labels for a given dataset (in addition to the regular strain_mappings.csv file), and during loading optionally discard any metabolomics objects...
In addition to #11, it would also be important for the output from nplinker to include all the information required to reproduce the results. This could include at least: -...
At the moment we can group spectra according to the molecular family ID that comes from the GNPS output. But we should be able to handle any form of grouping,...
what kind of output (and in what format) should we provide the user. Simon's initial thought would be that for any pair of GCF and Spectrum (or group of spectra,...