Commits · master · Zeller Group / GECCO · GitLab

13 May, 2022 3 commits
- Release v0.9.3 · 28c93359
  Martin Larralde authored May 13, 2022
  
  28c93359
- Bump `pyhmmer` dependency to `v0.6.0` · 90cbde89
  Martin Larralde authored May 13, 2022
  
  90cbde89
- Fix `HMMER.run` code to support annotating genes with duplicate name · 6fe0823d
  Martin Larralde authored May 13, 2022
  
  6fe0823d
28 Apr, 2022 1 commit
- Fix `gecco.cli` to lowercase file format given from CLI · f6656b7c
  Martin Larralde authored Apr 28, 2022
  
  f6656b7c
26 Apr, 2022 1 commit
- Bump `pyrodigal` dependency to `v1.0` · 133b0257
  Martin Larralde authored Apr 26, 2022
  
  133b0257
11 Apr, 2022 5 commits
- Release v0.9.2 · 8d4fd13a
  Martin Larralde authored Apr 11, 2022
  
  8d4fd13a
- Remove `cpus` kwarg from `ClusterCRF.predict_probabilities` method · a45aac57
  Martin Larralde authored Apr 11, 2022
  
  a45aac57
- Fix padding to add features on both ends and enable padding by default in CLI · 03fc3434
  Martin Larralde authored Apr 11, 2022
  
  03fc3434
- Improve display message when padding a small sequence in `ClusterCRF.predict_probabilities` · 1c0c35cd
  Martin Larralde authored Apr 07, 2022
  
  1c0c35cd
- Add CLI flag to `gecco run` to enable sequence padding manually · c7d1c36c
  Martin Larralde authored Apr 07, 2022
  
  c7d1c36c
07 Apr, 2022 1 commit
- Enable padding of small sequences with empty genes in `ClusterCRF` · ec05a768
  Martin Larralde authored Apr 07, 2022
  
  ec05a768
05 Apr, 2022 5 commits
- Update tests files for Galaxy tool wrapper · 140b4ff9
  Martin Larralde authored Apr 06, 2022
  
  140b4ff9
- Release v0.9.1 · c79bc696
  Martin Larralde authored Apr 05, 2022
  
  c79bc696
- Change default probability threshold for segmentation from 0.3 to 0.8 · 40ad5fc4
  Martin Larralde authored Apr 05, 2022
  
  40ad5fc4
- Update Galaxy tool wrapper in prevision for the next version of GECCO · 687f7de3
  Martin Larralde authored Apr 05, 2022
  
  687f7de3
- Update `gecco annotate` and `gecco run` to force TSV output even when no... · 11f30971
  Martin Larralde authored Apr 05, 2022
```
Update `gecco annotate` and `gecco run` to force TSV output even when no gene/features/clusters are found
```
  11f30971
31 Mar, 2022 5 commits
- Bump Sphinx version used to build documentation · 68cb45a8
  Martin Larralde authored Apr 01, 2022
  
  68cb45a8
- Update documentation index to mention the `genes.tsv` file [ci skip] · 1d324f64
  Martin Larralde authored Apr 01, 2022
  
  1d324f64
- Fix feature and gene tables not containing contigs too short to be processed by the CRF · 9e7465ba
  Martin Larralde authored Apr 01, 2022
  
  9e7465ba
- Release v0.9.1-alpha4 · f80616db
  Martin Larralde authored Mar 31, 2022
  
  f80616db
- Train CRF with optimal window size and feature selection values · 31b18bde
  Martin Larralde authored Mar 31, 2022
  
  31b18bde
28 Mar, 2022 6 commits
- Release v0.9.1-alpha3 · bc42a4a6
  Martin Larralde authored Mar 28, 2022
  
  bc42a4a6
- Refactor common code of table objects into a base class · c5a66454
  Martin Larralde authored Mar 28, 2022
  
  c5a66454
- Update `gecco train` to expect a gene table instead of a GFF file · 48ecbdd4
  Martin Larralde authored Mar 28, 2022
  
  48ecbdd4
- Fix implementation of `GeneTable.to_genes` · 3515efb4
  Martin Larralde authored Mar 28, 2022
  
  3515efb4
- Update `gecco run` and `gecco annotate` to output a gene table · 5e1088d5
  Martin Larralde authored Mar 28, 2022
  
  5e1088d5
- Add new `GeneTable` class to store gene-by-gene coordinates and probabilities · f6282752
  Martin Larralde authored Mar 28, 2022
  
  f6282752
23 Mar, 2022 2 commits
- Release v0.9.1-alpha2 · 7970c073
  Martin Larralde authored Mar 23, 2022
  
  7970c073
- Update `TypeClassifier.trained` to load empty or unknown types as `ProductType.Unknown` · 6f2d4f10
  Martin Larralde authored Mar 23, 2022
  
  6f2d4f10
21 Mar, 2022 1 commit
- Fix unexpected success in `tests.test_cli.test_run` · 8b826de3
  Martin Larralde authored Mar 21, 2022
  
  8b826de3
20 Mar, 2022 10 commits
- Release v0.9.1-alpha1 · f990a94e
  Martin Larralde authored Mar 20, 2022
  
  f990a94e
- Fix extraction unknown types in `gecco.types.TypeClassifier.trained` · a9a65b0f
  Martin Larralde authored Mar 20, 2022
  
  a9a65b0f
- Update embedded model with a temporary one trained on GECCO-data v0.9.1 · 95b8366c
  Martin Larralde authored Mar 20, 2022
  
  95b8366c
- Bump Pfam HMM to `v35.0` · ee9aeb4d
  Martin Larralde authored Mar 20, 2022
  
  ee9aeb4d
- Add missing docstring to `gecco.model.Gene.with_probability` · 3edd8e56
  Martin Larralde authored Mar 20, 2022
  
  3edd8e56
- Mark some tests as expected failures in `tests/test_cli` until next model is trained · f157182e
  Martin Larralde authored Mar 20, 2022
  
  f157182e
- Update `ClusterCRF.predict_probabilities` to skip contigs too small for prediction with a warning · 8d1b43d1
  Martin Larralde authored Mar 20, 2022
  
  8d1b43d1
- Remove `--overlap` flag from `gecco train` and make `CRF.fit` crash on training sequences too small · 6010d05d
  Martin Larralde authored Mar 20, 2022
  
  6010d05d
- Update `gecco train` CLI to allow setting sliding window size and step when training · 33359a4d
  Martin Larralde authored Mar 20, 2022
  
  33359a4d
- Disable the contig edge filter in `gecco run` command by default · 005167a2
  Martin Larralde authored Mar 20, 2022
  
  005167a2