nplinker documentation (WIP)¶
NPLinker module¶
Scoring methods¶
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class
nplinker.scoring.methods.LinkCollection(and_mode=True)¶ Class which stores the results of running one or more scoring methods.
It provides access to the set of objects which were found to have links, the set of objects linked to each of those objects, and the information produced by the scoring method(s) about each link.
There are also some useful utility methods to filter the original results.
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class
nplinker.scoring.methods.ObjectLink(source, target, method, data=None, shared_strains=[])¶ Class which stores information about a single link between two objects.
There will be at most one instance of an ObjectLink for a given pair of objects (source, target) after running 1 or more scoring methods. Some methods, e.g. Metcalf, will always produce a single output per link. However other methods like Rosetta may find multiple “hits” for a given pair. In either case the data for a given method is associated with the ObjectLink so it can be retrieved afterwards.
- The information stored is basically:
- the “source” of the link (original object provided as part of the input)
- the “target” of the link (linked object, as determined by the method(s) used)
- a (possibly empty) list of Strain objects shared between source and target
- the output of the scoring method(s) used for this link (e.g. a metcalf score)