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Pull kmer length and recoding alphabet from model in search mode #80

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wichne opened this issue Sep 8, 2022 · 0 comments
Open

Pull kmer length and recoding alphabet from model in search mode #80

wichne opened this issue Sep 8, 2022 · 0 comments
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@christinehc

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@wichne
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wichne commented Sep 8, 2022

Users won't know parameters used to build model. That information is encoded in the model object, however.
Search mode should not require user parameterization. Instead that information should be read directly from the model being searched. If more than one model is being searched, might be a good idea to check if they were all built using the same parameters.
christinehc added a commit that referenced this issue Oct 4, 2023
@christinehc
feat: add k, alphabet as SnekmerModel properties (#80))
3b75c0d 
changelog:
- `k`, `alphabet`, and `alphabet_name` are now properties of `snekmer.model.SnekmerModel` object
  - The above properties can be set via standard property setters
- `step_name` and `snekmer_version` have been converted to properties rather than attributes. This designation is more suitable for the type of information being stored.
- `model_params` has been added as an attribute of `snekmer.model.SnekmerModel` object to prevent separate `AttributeError` issue
- addresses #80
christinehc added a commit that referenced this issue Oct 4, 2023
@christinehc
feat: add io.ModelLoader to load model objects (#80)
4b7fea3 
changelog:
- previous method of loading objects via direct unpickling does not correctly preserve properties and the property getter will no longer work.
- an explicit model loader object has been written to correctly inherit properties and prevent the above. Will be necessary to correctly pull these properties for future Snekmer search update.
- addresses #80
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