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Remove strain assignment from BGC loaders? #104

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Tracked by #147
CunliangGeng opened this issue Feb 15, 2023 · 2 comments
Closed
3 tasks done
Tracked by #147

Remove strain assignment from BGC loaders? #104

CunliangGeng opened this issue Feb 15, 2023 · 2 comments
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GEN genomics related issues MET metabolomics related issues

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@CunliangGeng
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CunliangGeng commented Feb 15, 2023

Strain object is initiated and assigned to BGC object in BGC loaders, like MibigBGCLoader and AntismashBGCLoader.
It makes more sense to init strain objects and assign it to BGC outside of BGC loaders.

  • check the logics of strain loading
  • check the assignment of strain to BGC, spec and other objects
  • assign strain to BGC outside of BGC loaders.

To solve this issue after refactoring of strain mapping loading and GCF loading.

@CunliangGeng CunliangGeng added GEN genomics related issues MET metabolomics related issues labels Feb 15, 2023
@hechth
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hechth commented Feb 24, 2023

The strain objects in form of a StrainCollection are also passed to the metabolomics loading - I think it makes sense to load the strains afterwards and then add them after loading the metabolomics and genomics seperately.

@CunliangGeng
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Solved in #197.

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Labels
GEN genomics related issues MET metabolomics related issues
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