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153 bgc mappings generation #155

Merged
merged 117 commits into from
Jul 4, 2023
Merged

153 bgc mappings generation #155

merged 117 commits into from
Jul 4, 2023

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CunliangGeng
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@CunliangGeng CunliangGeng commented Jul 3, 2023 •
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To resolve #153

Notice

  1. Please review PR clean up loader and downloader #149 first. Review this one after PR 149 is merged.
    2. The first commit of this PR is 4b7dab9

@CunliangGeng
change BGC attributes type from list to tuple
742d4b5 
The following BGC attributes are updated:
- product_prediction
- mibig_bgc_class
- smiles
@CunliangGeng
use positional-only parameter in BGC and GCF
f1cac59 
Parameters before "/" are positional-only parameters, see https://docs.python.org/3/glossary.html#term-parameter.
@CunliangGeng
update BGC's __eq__ and __hash__
18e77a6
@CunliangGeng
update GCF's __eq__ and __hash__
da2cf41
@CunliangGeng
Update gcf.py
2111e5b
@CunliangGeng
update Spectrum's __eq__ and __hash__
0736476
@CunliangGeng
update MolecularFamily __eq__ and __hash__
fda1208
@CunliangGeng
Update molecular_family.py
0a7ccee
@CunliangGeng
update Strain __eq__ and __hash__
6a373e1
@CunliangGeng
update StrainCollection __eq__
33ed3c6
@CunliangGeng
add TODO comments to ObjectLink
f6bae56
@CunliangGeng
add parameter type check for add_alias
f81accf
@CunliangGeng
add __contains__ to Strain class
53dad82
@CunliangGeng
update lookup method of StrainCollection
45d8765
@CunliangGeng
update __contains__ in StrainCollection
7cb75e0
@CunliangGeng
remove from __eq__
f797ee5
@CunliangGeng
update __eq__ logic for Strain
8a3fa1b
@CunliangGeng
rename _strain_dict_id to _strain_dict_name in StrainCollection
8875400
@CunliangGeng
add comments to get_common_strains
2f77539
@CunliangGeng
add comments and rename variables for DataLinks
dae421d
@CunliangGeng
add comment about met_only parameter
504862e
@CunliangGeng
add todo comments to LinkFinder
8b160e6
@CunliangGeng
add comments to GNPSSpectrumLoader
8e9557c 
to figure out how `spectrum_id` is set
@CunliangGeng
change Spectrum.spectrum_id from type int to str
9257e0b
@CunliangGeng
update spec_dict
43f6d80
@CunliangGeng
Update tests
7536e42
@CunliangGeng
update __eq__ in MolecularFamily
a0cf97a
@CunliangGeng
change MolecularFamily.family_id from type int to str
b53af96
@CunliangGeng
add method has_strain to MolecularFamily
ca848fd
@CunliangGeng
Update metcalf_scoring.py
583fa33
@CunliangGeng
update exception type
42d7128
@CunliangGeng
refactor the usage of PODPDownloader
3065ec7 
1. create instance in the private method, only when it's needed
2. change the scope of the instance from global to local
@CunliangGeng
rename private config attributes in class DatasetLoader
f0c6b21 
-  add prefix `_config` for all config attributes
- add comments to restructure `__init__` code
@CunliangGeng
change the variable of app data dir to be global
6fc3d16 
this variable is independent of DatasetLoader and other classes, so it should be a global variable
@CunliangGeng
change two public methods to variables
5e0202e
@CunliangGeng
change one public method to attribute for DatasetLoader
2180461
@CunliangGeng
add value validation to Config
e0c8aeb 
- move the validation of antismash format config in DatasetLoader to Config class
- refactor the config data validations into a private method
@CunliangGeng
add TODO comments about init and validate paths
5ab6b95
@CunliangGeng
remove unused attribute growth_media
98c3a2f
@CunliangGeng
remove commented code
88f6f2a
@CunliangGeng
add TODO comments
9691b2f
@CunliangGeng
remove unused imports
765003b
@CunliangGeng
format the code
30ce79c
@CunliangGeng
reorder methods in loader.py
3002ae6
@CunliangGeng
Merge branch 'dev' into cleanup_loader
87cc2de
@CunliangGeng
add function generate_genome_bgc_mappings_file
4b7dab9
@CunliangGeng
Update __init__.py
2499279
@CunliangGeng
add tests for generate_genome_bgc_mappings_file
5afa67e
@CunliangGeng
update strain test when 113 issue is closed
6d32c51
@CunliangGeng CunliangGeng requested a review from gcroci2 July 3, 2023 10:09
@CunliangGeng CunliangGeng linked an issue Jul 3, 2023 that may be closed by this pull request
implement the function to generate refseq id ↔ BGC id mapping file #153
Closed
@CunliangGeng CunliangGeng added this to the refactor codebase milestone Jul 3, 2023
@CunliangGeng CunliangGeng marked this pull request as ready for review July 3, 2023 10:10
@CunliangGeng CunliangGeng merged commit 721e125 into dev Jul 4, 2023
@CunliangGeng CunliangGeng deleted the 153_bgc_mappings_generation branch July 4, 2023 13:45
hechth
hechth reviewed Jul 6, 2023
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Nice refactorings!

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@hechth hechth hechth left review comments

@gcroci2 gcroci2 gcroci2 approved these changes

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implement the function to generate refseq id ↔ BGC id mapping file
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@CunliangGeng @hechth @gcroci2