Update loading of genomics data #197

CunliangGeng · 2023-12-12T10:51:20Z

Update the genomics loading process and helper functions, making sure they are consistent with those for loading metatbolomics.

Major changes:

update the assignment of attributes self.bgcs and self.gcfs to make sure they contain valid BGC/GCF objects that have Strain objects added
remove and update helper functions
update unit tests on helper functions

CunliangGeng · 2023-12-12T10:51:50Z

Current dependencies on/for this PR:

dev
- PR refactor filtering of user specified strains #178
  - PR Enable GCF loader to filter singleton GCFs #181
    - PR return list for get_bgcs methods of BGC loaders #182
      - PR rename strains.py to strain.py #183
        
        PR remove deprecated functions of loading genomics data #184
        
        PR update the process of loading genomics data #185
        
        PR rename genomics.py to utils.py #186
        
        PR remove deprecated functions of loading metabolomics data #187
        
        PR refactor class MolecularFamily #188
        PR refactor class GCF #189
        PR enable parallel testing using pytest-xdist #190
        PR Enable filtering of singleton molecular families #191
        PR Remove class SingletonFamily and MF attribute id #192
        PR refactor Spectrum class #193
        PR remove unused mgf.py and its test file #194
        PR Update logics of loading metabolomics data #196
        PR Update loading of genomics data #197 👈
        PR deprecate the method _load_class_info #198
        PR remove loading of optional data #199
        PR remove filtering of common strains during loading #200
        PR update logics of loading mibig data #201
        PR refactor initiation of paths to metabolomics files #202
        
        PR Update logics of loading metabolomics data #195

This stack of pull requests is managed by Graphite.

.vscode/settings.json

CunliangGeng · 2024-01-24T15:20:39Z

Merge activity

Jan 24, 10:20 AM: @CunliangGeng started a stack merge that includes this pull request via Graphite.
Jan 24, 10:21 AM: Graphite rebased this pull request as part of a merge.
Jan 24, 10:22 AM: @CunliangGeng merged this pull request with Graphite.

- add the missing comma - the values were updated automatically based on latest schema of vscode

Change raising not found error to only logging it.

- remove raising errors - add logging info - add return values

CunliangGeng mentioned this pull request Dec 12, 2023

Update logics of loading metabolomics data #196

Merged

CunliangGeng requested a review from gcroci2 December 12, 2023 10:57

CunliangGeng force-pushed the 12-11-update_loading_genomics branch from c4d78bc to ede6a9a Compare December 12, 2023 11:02

This was referenced Dec 12, 2023

deprecate the method _load_class_info #198

Merged

remove loading of optional data #199

Merged

remove filtering of common strains during loading #200

Merged

CunliangGeng force-pushed the 12-04-update_loading_metabolomics branch from a1be676 to b636ccb Compare December 14, 2023 08:33

CunliangGeng force-pushed the 12-11-update_loading_genomics branch from ede6a9a to ed4d425 Compare December 14, 2023 08:33

CunliangGeng force-pushed the 12-04-update_loading_metabolomics branch from b636ccb to d736891 Compare December 14, 2023 10:00

CunliangGeng force-pushed the 12-11-update_loading_genomics branch from ed4d425 to 36816a7 Compare December 14, 2023 10:00

CunliangGeng force-pushed the 12-04-update_loading_metabolomics branch from d736891 to 9c4f3d1 Compare December 19, 2023 13:21

CunliangGeng force-pushed the 12-11-update_loading_genomics branch from 36816a7 to bc05232 Compare December 19, 2023 13:21

CunliangGeng force-pushed the 12-04-update_loading_metabolomics branch from 9c4f3d1 to 5354122 Compare December 19, 2023 13:38

CunliangGeng force-pushed the 12-11-update_loading_genomics branch from bc05232 to 83f8e39 Compare December 19, 2023 13:38

This was referenced Dec 20, 2023

update logics of loading mibig data #201

Merged

refactor initiation of paths to metabolomics files #202

Merged

gcroci2 approved these changes Dec 21, 2023

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Base automatically changed from 12-04-update_loading_metabolomics to dev January 24, 2024 15:21

CunliangGeng added 6 commits January 24, 2024 15:21

update vscode settings.json

c695898

- add the missing comma - the values were updated automatically based on latest schema of vscode

update helper function add_strain_to_bgc

c24ee93

Change raising not found error to only logging it.

update helper function add_bgc_to_gcf

6a2fee4

- remove raising errors - add logging info - add return values

remove helper functions get_bgcs_from_gcfs and get_strains_from_bgcs

75be69e

Update test_utils.py

3b7d6d5

update the assignment of attributes self.bgcs and self.gcfs

c3bc259

CunliangGeng force-pushed the 12-11-update_loading_genomics branch from 83f8e39 to c3bc259 Compare January 24, 2024 15:21

CunliangGeng merged commit 9e3d296 into dev Jan 24, 2024
1 of 2 checks passed

CunliangGeng deleted the 12-11-update_loading_genomics branch January 24, 2024 15:22

CunliangGeng mentioned this pull request Feb 2, 2024

Remove strain assignment from BGC loaders? #104

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Update loading of genomics data #197

Update loading of genomics data #197

CunliangGeng commented Dec 12, 2023 •

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CunliangGeng commented Jan 24, 2024 •

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Update loading of genomics data #197

Update loading of genomics data #197

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CunliangGeng commented Dec 12, 2023 • edited Loading

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CunliangGeng commented Jan 24, 2024 •

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