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Refactor loading genomics #168

Merged
merged 21 commits into from
Aug 24, 2023
Merged

Refactor loading genomics #168

merged 21 commits into from
Aug 24, 2023

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CunliangGeng
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This PR intends to refactor the loading of strain mappings for genomics part, which involves the loading of not only the strain mappings but also genomics data (e.g. BGC, GCF).

The major changes:

  • Update the logics of DatasetLoader._load_genomics method with newly created/refactored functions/classes
  • Update the logics of StrainCollection methods add, remove and lookup
  • Update or add methods to classes GCF, MibigBGCLoader, Strain and StrainCollection

Expected Failed test: test_load_metabolomics

@CunliangGeng
remove useless step
8e4dcd8
@CunliangGeng
remove completed TODO comment
4917161
@CunliangGeng
remove param bgc_genome_mapping from func map_strain_to_bgc
afd81e5 
The StrainCollection should contains the bgc id, so genome id is not required.
@CunliangGeng
add property names to class Strain
21cd0fc
@CunliangGeng
update the logic of method __contains__ in StrainCollection
3485155
@CunliangGeng
add method has_name to class StrainCollection
1211657
@CunliangGeng
update method has_strain in classes
14b3453
@CunliangGeng
rename MibigBGCLoader to MibigLoader
ab226d5
@CunliangGeng
rename method get_bgc_genome_mapping to get_strain_bgc_mapping
1058928
@CunliangGeng
refactor mibig loading related code to _load_mibig method
36fda27
@CunliangGeng
remove mibig downloading in class DatasetLoader
c668ca8
@CunliangGeng
refactor bigscape running code to _run_bigscape
a9b808f
@CunliangGeng
refactor method _load_genomics
682a0a5
@CunliangGeng
add TODO comments
0991a47
@CunliangGeng
add TODO comment
70e1640
@CunliangGeng
change StrainCollection._strain_dict_name dict value type to list
10364ef 
- Updated methods `add`, `remove` and `lookup` accordingly
- Updated and added unit tests for updated methods
@CunliangGeng
update references of method StrainCollection.lookup
43d7f23
@CunliangGeng CunliangGeng self-assigned this Aug 23, 2023
@CunliangGeng CunliangGeng mentioned this pull request Aug 23, 2023
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gcroci2
gcroci2 approved these changes Aug 24, 2023
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I left very minor comments :)

tests/test_strain.py Show resolved Hide resolved
src/nplinker/strain_collection.py Outdated Show resolved Hide resolved
tests/test_strain_collection.py Show resolved Hide resolved
@CunliangGeng CunliangGeng merged commit 80a8299 into dev Aug 24, 2023
2 of 4 checks passed
@CunliangGeng CunliangGeng deleted the refactor_loading_genomics branch August 24, 2023 15:20
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@gcroci2 gcroci2 gcroci2 approved these changes

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@CunliangGeng @gcroci2