Commits · Hooft001-master-patch-88968 · bioinformatics / iPRESTO · GitLab

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Feb 15, 2023
- Update README.md · 635b4473
  Justin van der Hooft authored 2 years ago
  
  635b4473
Aug 18, 2022
- Update output message · c5e7d940
  Louwen, Joris authored 2 years ago
  
  c5e7d940
- Update usage · 7b69a6d3
  Louwen, Joris authored 2 years ago
  
  7b69a6d3
Aug 10, 2022
- add back --use_domtabs to circumvent lack of hmmer in test env · eeb80e07
  louwenjjr authored 2 years ago
  
  eeb80e07
- succesfully test querying with presto-top and add existing lda_model to test_subclusters to do so · 11b683b3
  louwenjjr authored 2 years ago
  
  11b683b3
Aug 02, 2022
- Update Readme according to refactoring. · 99ff81e2
  Louwen, Joris authored 2 years ago
  
  99ff81e2
- Merge branch 'ipresto_refactor' into 'master' · 25efa7e8
  Louwen, Joris authored 2 years ago
  25efa7e8
- Merge branch 'ipresto_refactor' of https://git.wur.nl/bioinformatics/iPRESTO into ipresto_refactor · 5ad64f9d
  louwenjjr authored 2 years ago
  
  5ad64f9d
- improve documentation · 2f1e9822
  louwenjjr authored 2 years ago
  
  2f1e9822
- prevent overriding gbks_path_file · c47ee60e
  louwenjjr authored 2 years ago
  
  c47ee60e
- discover stats about annotated subcluster motifs · 791f6b4b
  louwenjjr authored 2 years ago
  
  791f6b4b
- updates to training multiple lda models · 7e317900
  louwenjjr authored 2 years ago
  
  7e317900
May 12, 2022
- Correct typo · 15c618b1
  Louwen, Joris authored 3 years ago
  
  15c618b1
- Add use_domtabs to all ipresto.py tests so hmmscan is not attempted in test environment · d05d4b7d
  Louwen, Joris authored 3 years ago
  
  d05d4b7d
- Add domtables for test bgcs so hmmscan doesnt have to be run in test env · fff8282b
  louwenjjr authored 3 years ago
  
  fff8282b
- Specify gensim version to 3.8.3 · 4e988e63
  Louwen, Joris authored 3 years ago
  
  4e988e63
- Replace build stage with before_script in .gitlab-ci.yml file · b760be0d
  Louwen, Joris authored 3 years ago
  
  b760be0d
- Add valid python image in .gitlab-ci.yml file · 1cb9cbfd
  Louwen, Joris authored 3 years ago
  
  1cb9cbfd
- Update .gitlab-ci.yml file · c72f697e
  Louwen, Joris authored 3 years ago
  
  c72f697e
May 03, 2022
- Init basic .gitlab-ci.yml file · f4ccf144
  Louwen, Joris authored 3 years ago
  
  f4ccf144
Mar 17, 2022
- Allow testing for alpha and beta values of lda model · 943d1806
  Louwen, Joris authored 3 years ago
  
  943d1806
Mar 14, 2022
- Try out different parameters · 4bb37b6c
  Louwen, Joris authored 3 years ago
  
  4bb37b6c
- Unify remove_infr_doms functions · 5a542df5
  Louwen, Joris authored 3 years ago
  
  5a542df5
Mar 10, 2022
- turn off sorting topics in lda vis so topic numbers correspond · 6cdcecdf
  Louwen, Joris authored 3 years ago
  
  6cdcecdf
Mar 02, 2022
- add outfolder parameter to run_lda_from_existing to reflect changes in previous commit · fece3423
  Louwen, Joris authored 3 years ago
  
  fece3423
- save corpus · ba17e4ea
  Louwen, Joris authored 3 years ago
  
  ba17e4ea
- remove bgcs_and_modules output, add modules_w_info when querying and making... · 8a7cd5f7
  Louwen, Joris authored 3 years ago
  8a7cd5f7
Jan 21, 2022
- correct to use --visualise_subclusters properly - if statement was wrong way around · e4d342e6
  Louwen, Joris authored 3 years ago
  
  e4d342e6
Nov 24, 2021
- linting · 1d08deda
  Louwen, Joris authored 3 years ago
  
  1d08deda
- add step 5. visualise subclusters, add verbose to arrower · be21ab1f
  Louwen, Joris authored 3 years ago
  
  be21ab1f
- keep plots from crashing when there are no matches + linting · 8e41a199
  Louwen, Joris authored 3 years ago
  
  8e41a199
- include presto_top · b7327c33
  Louwen, Joris authored 3 years ago
  
  b7327c33
Nov 22, 2021
- linting · cf2211c2
  Louwen, Joris authored 3 years ago
  
  cf2211c2
- linting, moving presto_stat functionality to ipresto.py and query_statistical_modules.py · 3274ae3f
  Louwen, Joris authored 3 years ago
  
  3274ae3f
- test subclusters to test the --stat_subclusters flag · caeb46fb
  Louwen, Joris authored 3 years ago
  
  caeb46fb
- linting · 0a3726ad
  Louwen, Joris authored 3 years ago
  
  0a3726ad
- include running PRESTO-STAT for predetermined subclusters (to use with --stat_subclusters) + tests · 32d2144c
  Louwen, Joris authored 3 years ago
  
  32d2144c
Nov 19, 2021
- add prints for general steps, linting · 6ec7c732
  Louwen, Joris authored 3 years ago
  
  6ec7c732
- temporarily remove CI pipeline while runners are not set up · 61d27f14
  Louwen, Joris authored 3 years ago
  
  61d27f14
- Revert "Temporarily comment out .gitlab-ci.yml until runners are set up" · d5e069ca
  Louwen, Joris authored 3 years ago
  d5e069ca