Update logics of loading metabolomics data #195

CunliangGeng · 2023-12-05T15:28:50Z

Major changes:

update loading process in DatasetLoader._load_metabolomics.
add utility functions for metabolomics loading

Add keep_singleton to the base class of GCF loader

- change returned value from dict to list for `MibigLoader.get_bgcs` method and the underlying method `._parse_bgcs` - update the use of the changed methods - update unit tests

- change returned value from dict to list for `AntismashBGCLoader.get_bgcs` method and the underlying method `._parse_bgcs` - update the use of the changed methods - update unit tests

This function is needed anymore. GCF loader already has the functionality to filter mibig only GCF during loading.

CunliangGeng · 2023-12-05T15:29:22Z

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.

- remove `None` from typing and keep only `float` - change default value to 0 - update spectrum loader

- remove argument `annotations` - remove property `gnps_annotations` - add attribute `gnps_annotations`

…thod

…PLinker/nplinker into 12-04-update_load_metabolomics

CunliangGeng · 2023-12-11T13:17:24Z

Commits from previous PRs are mixed in this PR. Close it now, will create a new one with clean commits (see #196).

CunliangGeng added 14 commits November 20, 2023 10:08

add method is_singleton to GCF class

1a5436d

add param keep_singleton to method GCFLoaderBase.get_gcfs

8b4e025

Add keep_singleton to the base class of GCF loader

add param keep_singleton to bigscape GCF loader

e95827f

simplify gcf test data file

ace02d6

update unit tests for bigscape gcf loader

5139465

update base class BGCLoaderBase

7020f47

change the returned type of MibigLoader.get_bgcs

dfb1720

- change returned value from dict to list for `MibigLoader.get_bgcs` method and the underlying method `._parse_bgcs` - update the use of the changed methods - update unit tests

change the returned type of AntismashBGCLoader.get_bgcs

17f8ac3

- change returned value from dict to list for `AntismashBGCLoader.get_bgcs` method and the underlying method `._parse_bgcs` - update the use of the changed methods - update unit tests

rename strains.py to strain.py

41343c0

ruff fix imports order

dc2efbe

remove deprecated function load_gcfs

3eadaa5

remove function filter_mibig_only_gcf

3d8330a

This function is needed anymore. GCF loader already has the functionality to filter mibig only GCF during loading.

update the loading of genomics data

1d54709

rename genomics.py to utils.py

1ddfb6f

CunliangGeng added 13 commits December 5, 2023 16:51

remove property normalised_peaks

d64c41e

change default value of argument rt

6c70cb9

- remove `None` from typing and keep only `float` - change default value to 0 - update spectrum loader

remove arg annotations and add attribute gnps_annotations

8dacec3

- remove argument `annotations` - remove property `gnps_annotations` - add attribute `gnps_annotations`

remove unused global variable GNPS_KEY

320364c

add typing for attribute gnps_id

c950277

add typings and docstring for strains attribute and has_strain me…

453f092

…thod

update class docstrings

936e2ae

update Spectrum loader

a869438

add unit tests for Spectrum class

54a9f64

remove unused mgf.py and its test file

7c9daaa

add utilities for loading metabolomics data

7d8686c

Create test_utils.py

1c1e060

update logics of loading metabolomics data

9a322a7

CunliangGeng force-pushed the 12-04-remove_unused_mgf_parser branch from 043e2e5 to 7c9daaa Compare December 5, 2023 15:54

CunliangGeng force-pushed the 12-04-update_load_metabolomics branch from 9b499d4 to 9a322a7 Compare December 5, 2023 15:54

CunliangGeng added 4 commits December 11, 2023 11:03

add utilities for loading metabolomics data

fe2f958

Create test_utils.py

a24d170

update logics of loading metabolomics data

5d8407f

Merge branch '12-04-update_load_metabolomics' of https://github.com/N…

d8b113b

…PLinker/nplinker into 12-04-update_load_metabolomics

CunliangGeng force-pushed the 12-04-remove_unused_mgf_parser branch from 7c9daaa to d633acd Compare December 11, 2023 13:04

CunliangGeng closed this Dec 11, 2023

CunliangGeng deleted the 12-04-update_load_metabolomics branch December 11, 2023 13:17

This was referenced Dec 11, 2023

Update logics of loading metabolomics data #196

Merged

Update loading of genomics data #197

Merged

deprecate the method _load_class_info #198

Merged

remove loading of optional data #199

Merged

remove filtering of common strains during loading #200

Merged

This was referenced Dec 20, 2023

update logics of loading mibig data #201

Merged

refactor initiation of paths to metabolomics files #202

Merged

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Update logics of loading metabolomics data #195

Update logics of loading metabolomics data #195

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Update logics of loading metabolomics data #195

Update logics of loading metabolomics data #195

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