Commits · master · Zeller Group / GECCO · GitLab

01 Sep, 2022 2 commits
- Fix change in coverage report format in `.gitlab-ci.yml` · 5851e27f
  Martin Larralde authored Sep 01, 2022
  
  5851e27f
- Fix missing `gzip` import in `gecco.cli.commands._mixins` · c82285b3
  Martin Larralde authored Sep 01, 2022
  
  c82285b3
18 Aug, 2022 1 commit
- Add `CITATION.cff` file with bioRXiv preprint reference [ci skip] · 104ad186
  Martin Larralde authored Aug 19, 2022
  
  104ad186
10 Aug, 2022 1 commit
- Release v0.9.5 · b60eaf77
  Martin Larralde authored Aug 10, 2022
  
  b60eaf77
29 Jun, 2022 1 commit
- Make `gecco.orf` handle STOP codons consistently · ba4d1c56
  Martin Larralde authored Jun 29, 2022
  
  ba4d1c56
25 Jun, 2022 2 commits
- Reduce memory consumption in `gecco predict` by dropping unknown sequences · 516840aa
  Martin Larralde authored Jun 25, 2022
  
  516840aa
- Rewrite sequence loading mixin in CLI to load record with an iterator · 095562d9
  Martin Larralde authored Jun 25, 2022
  
  095562d9
23 Jun, 2022 4 commits
- Fix issues with antiSMASH sideload JSON file generation in `gecco run` and `gecco predict` · 2b33a0cc
  Martin Larralde authored Jun 23, 2022
  
  2b33a0cc
- Fix probabilities not being extracted from feature table input in `gecco predict` · 12ffd489
  Martin Larralde authored Jun 23, 2022
  
  12ffd489
- Add support for merging GenBank records inside a single output file · 6f5bd521
  Martin Larralde authored Jun 23, 2022
  
  6f5bd521
- Add `Protein.with_seq` function to assign a new sequence to a protein object · d4601b26
  Martin Larralde authored Jun 23, 2022
  
  d4601b26
22 Jun, 2022 3 commits
- Refactor common code for building an output directory into a dedicated class · 118fa862
  Martin Larralde authored Jun 23, 2022
  
  118fa862
- Reorganize shared code between CLI commands into mixin classes · eb94846a
  Martin Larralde authored Jun 23, 2022
  
  eb94846a
- Add a dedicated command to predict BGCs from an already annotated genome · f75d12ce
  Martin Larralde authored Jun 22, 2022
  
  f75d12ce
31 May, 2022 5 commits
- Release v0.9.4 · 3c64b104
  Martin Larralde authored May 31, 2022
  
  3c64b104
- Update internal InterPro metadata file and remove Tigrfam entries · dd9614c2
  Martin Larralde authored May 31, 2022
  
  dd9614c2
- Mention the `genes.tsv` file in `README.md` [ci skip] · f8091a8d
  Martin Larralde authored May 31, 2022
  
  f8091a8d
- Fix gene coordinates in `CDSFinder` and add tests for gene feature extraction · b9406749
  Martin Larralde authored May 31, 2022
  
  b9406749
- Fix `pydocstyle` issues in `gecco.model` introduced by type hints · 2ffbdeb9
  Martin Larralde authored May 30, 2022
  
  2ffbdeb9
30 May, 2022 17 commits
- Delegate import of `numpy` type annotations for Python 3.6 compatibility · 07530de1
  Martin Larralde authored May 30, 2022
  
  07530de1
- Fix all remaining type annotations in `gecco.cli` module · 6811312a
  Martin Larralde authored May 30, 2022
  
  6811312a
- Fix remaining type annotations in main `gecco` modules · 4d719aa5
  Martin Larralde authored May 30, 2022
  
  4d719aa5
- Bump minimum `rich` to `12.3` to use `None` total in progress bars · eea3b6c1
  Martin Larralde authored May 30, 2022
  
  eea3b6c1
- Fix minor issues identified by `mypy` and correct some type annotations · a25c1cdc
  Martin Larralde authored May 30, 2022
  
  a25c1cdc
- Fix some type annotations issues in `gecco.model`, `gecco.crf` and `gecco.hmmer` modules · 68d57325
  Martin Larralde authored May 30, 2022
  
  68d57325
- Fix missing docstrings in new `ProductType` implementation · 920beaf7
  Martin Larralde authored May 30, 2022
  
  920beaf7
- Fix broken tests for progress callback of `PyrodigalFinder` · cb7ee06b
  Martin Larralde authored May 30, 2022
  
  cb7ee06b
- Allow specifying custom exclusive HMMs from the GECCO command line · 6ece7653
  Martin Larralde authored May 30, 2022
  
  6ece7653
- Support exclusive HMMs retaining only the best-scoring domain annotation per gene · 362f5814
  Martin Larralde authored May 30, 2022
  
  362f5814
- Add support for CDS feature extraction in `gecco run` and `gecco annotate` · 93ef4543
  Martin Larralde authored May 30, 2022
  
  93ef4543
- Add support for specifying the protein ID qualifier in `CDSFinder` · 958167c7
  Martin Larralde authored May 30, 2022
  
  958167c7
- Update `CDSFinder` to report progress with the `progress` callback · 60a8fbc5
  Martin Larralde authored May 30, 2022
  
  60a8fbc5
- Implement an alternative `ORFFinder` extracting the features from annotated records · 8b86f8e3
  Martin Larralde authored May 30, 2022
  
  8b86f8e3
- Fix progress display in new `PyrodigalFinder._find_genes` · d8115a6d
  Martin Larralde authored May 30, 2022
  
  d8115a6d
- Update `PyrodigalFinder` to support training step when not in meta mode · 49f2a082
  Martin Larralde authored May 30, 2022
  
  49f2a082
- Refactor `PyrodigalFinder` without custom thread code · fb00fcd3
  Martin Larralde authored May 30, 2022
  
  fb00fcd3
27 May, 2022 4 commits
- Bump dependencies in `pyproject.toml` · 314194ce
  Martin Larralde authored May 27, 2022
  
  314194ce
- Make `gecco run` only predict type where there is more than one in the training data · f31d75a0
  Martin Larralde authored May 27, 2022
  
  f31d75a0
- Fix `tests.test_cli` and `tests.test_model` with new `ClusterTable` methods · 70d15720
  Martin Larralde authored May 27, 2022
  
  70d15720
- Fix `ClusterTable.dump` to work with optional probability columns · 16473c04
  Martin Larralde authored May 27, 2022
  
  16473c04