Mercurial > repos > althonos > gecco

view CHANGELOG.md @ 3:359232b58f6a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"Update Galaxy tool wrapper to follow the IUC best practices"
author althonos
date Sun, 21 Nov 2021 19:47:22 +0000
parents
children 169849dfb098
line wrap: on
line source

# Changelog
All notable changes to this project will be documented in this file.

The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).

## [Unreleased]
[Unreleased]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.5...master

## [v0.8.5] - 2021-11-21
[v0.8.5]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.4...v0.8.5
### Added
- Minimal compatibility support for running GECCO inside of Galaxy workflows.

## [v0.8.4] - 2021-09-26
[v0.8.4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.3-post1...v0.8.4
### Fixed
- `gecco convert gbk --format bigslice` failing to run because of outdated code ([#5](https://github.com/zellerlab/GECCO/issues/5)).
- `gecco convert gbk --format bigslice` not creating files with names conforming to BiG-SLiCE expected input.
### Changed
- Bump minimum `pyrodigal` version to `v0.6.2` to use platform-accelerated code if supported.

## [v0.8.3-post1] - 2021-08-23
[v0.8.3-post1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.3...v0.8.3-post1
### Fixed
- Wrong default value for `--threshold` being shown in `gecco run` help message.

## [v0.8.3] - 2021-08-23
[v0.8.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.2...v0.8.3
### Changed
- Default probability threshold for segmentation to 0.3 (from 0.4).

## [v0.9.0] - 2021-08-10 - **YANKED**
[v0.9.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.2...v0.9.0
### Changed
- Retrain internal model using `--select=0.35` instead of `--select=0.25` like before.
- Change default *p-value* filter from 1e-9 to 1e-5 to detect more features.

## [v0.8.2] - 2021-07-31
[v0.8.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.1...v0.8.2
### Fixed
- `gecco run` crashing on Python 3.6 because of missing `contextlib.nullcontext` class.
### Changed
- `gecco run` and `gecco annotate` will not try to count the number of profiles when given an external HMM file with the `--hmm` flag.
- `PyHMMER.run` now reports the *p-value* of each domain in addition to the *e-value* as a `/note` qualifier.

## [v0.8.1] - 2021-07-29
[v0.8.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.0...v0.8.1
### Changed
- `gecco run` now filters out unneeded features before annotating, making it easier to analyze the results of a run with a custom `--model`.
### Fixed
- `gecco` reporting about using Pfam `v33.1` while actually using `v34.0` because of an outdated field in `gecco/hmmer/Pfam.ini`.
### Added
- Missing documentation for the `strand` attribute of `gecco.model.Gene`.

## [v0.8.0] - 2021-07-03
[v0.8.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.7.0...v0.8.0
### Changed
- Retrain internal model using new sequence embeddings and remove broken/duplicate BGCs from MIBiG 2.0.
- Bump minimum `pyhmmer` version to `v0.4.0` to improve exception handling.
- Bump minimum `pyrodigal` version to `v0.5.0` to fix sequence decoding on some platforms.
- Use p-values instead of e-values to filter domains obtained with HMMER.
- `gecco cv` and `gecco train` now seed the RNG with a user-defined seed before shuffling rows of training data.
### Fixed
- Extraction of BGC compositions for the type predictor while training.
- `ClusterCRF.trained` failing to open an external model.
### Added
- `Domain.pvalue` attribute to access the p-value of a domain annotation.
- Mandatory `pvalue` column to `FeatureTable` objects.
- Support for loading several feature tables in `gecco train` and `gecco cv`.
- Warnings to `ClusterCRF.fit` when selecting uninformative features.
- `--correction` flag to `gecco train` and `gecco cv`, allowing to give a multiple testing correction method when computing p-values with the Fisher Exact Tests.
### Removed
- Outdated `gecco embed` command.
- Unused `--truncate` flag from the `gecco train` CLI.
- Tigrfam domains, which is not improving performance on the new training data.

## [v0.7.0] - 2021-05-31
[v0.7.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.3...v0.7.0
### Added
- Support for writing an AntiSMASH sideload JSON file after a `gecco run` workflow.
- Code for converting GenBank files in BiG-SLiCE compatible format with the `gecco convert` subcommand.
- Documentation about using GECCO in combination with AntiSMASH or BiG-SLiCE.
### Changed
- Minimum Biopython version to `v1.73` for compatibility with older bioinformatics tooling.
- Internal domain composition shipped in the `gecco.types` with newer composition array obtained directly from MIBiG files.
### Removed
- Outdated notice about `-vvv` verbosity level in the help message of the main `gecco` command.

## [v0.6.3] - 2021-05-10
[v0.6.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.2...v0.6.3
### Fixed
- HMMER annotation not properly handling inputs with multiple contigs.
- Some progress bar totals displaying as floats in the CLI.
### Changed
- `PyHMMER` now sets the `Z` and `domZ` values from the number of proteins given to the search pipeline.
- `gecco.cli` delegates imports to make CLI more responsive.
- `pkg_resources` has been replaced with `importlib.resources` and `importlib.metadata` where applicable.
- `multiprocessing.cpu_count` has been replaced with `os.cpu_count` where applicable.

## [v0.6.2] - 2021-05-04
[v0.6.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.1...v0.6.2
### Fixed
- `gecco cv loto` crashing because of outdated code.
### Changed
- Logging-style prompt will only display if GECCO is running with `-vv` flag.
### Added
- GECCO bioRxiv paper reference to `Cluster.to_seq_record` output record.

## [v0.6.1] - 2021-03-15
[v0.6.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.0...v0.6.1
### Fixed
- Progress bar not being disabled by `-q` flag in CLI.
- Fallback to using HMM name if accession is not available in `PyHMMER`.
- Group genes by source contig and process them separately in `PyHMMER` to avoid bogus E-values.
### Added
- `psutil` dependency to get the number of physical CPU cores on the host machine.
- Support for using an arbitrary mapping of positives to negatives in `gecco embed`.
### Removed
- Unused and outdated `HMMER` and `DomainRow` classes from `gecco.hmmer`.

## [v0.6.0] - 2021-02-28
[v0.6.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.5...v0.6.0
### Changed
- Updated internal model with a cleaned-up version of the MIBiG-2.0
  Pfam-33.1/Tigrfam-15.0 embedding.
- Updated internal InterPro catalog.
### Fixed
- Features not being grouped together in `gecco cv` and `gecco train`
  when provided with a feature table where rows were not sorted by
  protein IDs.

## [v0.5.5] - 2021-02-28
[v0.5.5]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.4...v0.5.5
### Fixed
- `gecco cv` bug causing only the last fold to be written.

## [v0.5.4] - 2021-02-28
[v0.5.4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.3...v0.5.4
### Changed
- Replaced `verboselogs`, `coloredlogs` and `better-exceptions` with `rich`.
### Removed
- `tqdm` training dependency.
### Added
- `gecco annotate` command to produce a feature table from a genomic file.
- `gecco embed` to embed BGCs into non-BGC regions using feature tables.

## [v0.5.3] - 2021-02-21
[v0.5.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.2...v0.5.3
### Fixed
- Coordinates of genes in output GenBank files.
- Potential issue with the number of CPUs in `PyHMMER.run`.
### Changed
- Bump required `pyrodigal` version to `v0.4.2` to fix buffer overflow.

## [v0.5.2] - 2021-01-29
[v0.5.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.1...v0.5.2
### Added
- Support for downloading HMM files directly from GitHub releases assets.
- Validation of filtered HMMs with MD5 checksum.
### Fixed
- Invalid coordinates of protein domains in GenBank output files.
- `gecco.interpro` module not being added to wheel distribution.
### Changed
- Bump required `pyhmmer` version to `v0.2.1`.

## [v0.5.1] - 2021-01-15
[v0.5.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.0...v0.5.1
### Fixed
- `--hmm` flag being ignored in in `gecco run` command.
- `PyHMMER` using HMM names instead of accessions, causing issues with Pfam HMMs.

## [v0.5.0] - 2021-01-11
[v0.5.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.5...v0.5.0
### Added
- Explicit support for Python 3.9.
### Changed
- [`pyhmmer`](https://pypi.org/project/pyhmmer) is used to annotate protein sequences instead of HMMER3 binary `hmmsearch`.
- HMM files are stored in binary format to speedup parsing and reduce storage size.
- `tqdm` is now a *training*-only dependency.
- `gecco cv` now requires *training* dependencies.

## [v0.4.5] - 2020-11-23
[v0.4.5]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.4...v0.4.5
### Added
- Additional `fold` column to cross-validation table output.
### Changed
- Use sequence ID instead of protein ID to extract type from cluster in `gecco cv`.
- Install HMM data in pre-pressed format to make `hmmsearch` runs faster on short sequences.
- `gecco.orf` was rewritten to extract genes from input sequences in parallel.

## [v0.4.4] - 2020-09-30
[v0.4.4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.3...v0.4.4
### Added
- `gecco cv loto` command to run LOTO cross-validation using BGC types
  for stratification.
- `header` keyword argument to `FeatureTable.dump` and `ClusterTable.dump`
  to write the table without the column header allowing to append to an
  existing table.
- `__getitem__` implementation for `FeatureTable` and `ClusterTable`
  that returns a single row or a sub-table from a table.
### Fixed
- `gecco cv` command now writes results iteratively instead of holding
  the tables for every fold in memory.
### Changed
- Bumped `pandas` training dependency to `v1.0`.

## [v0.4.3] - 2020-09-07
[v0.4.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.2...v0.4.3
### Fixed
- GenBank files being written with invalid `/cds` feature type.
### Changed
- Blocked installation of Biopython `v1.78` or newer as it removes `Bio.Alphabet`
  and breaks the current code.

## [v0.4.2] - 2020-08-07
[v0.4.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.1...v0.4.2
### Fixed
- `TypeClassifier.predict_types` using inverse type probabilities when
  given several clusters to process.

## [v0.4.1] - 2020-08-07
[v0.4.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.0...v0.4.1
### Fixed
- `gecco run` command crashing on input sequences not containing any genes.

## [v0.4.0] - 2020-08-06
[v0.4.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.3.0...v0.4.0
### Added
- `gecco.model.ProductType` enum to model the biosynthetic class of a BGC.
### Removed
- `pandas` interaction from internal data model.
- `ClusterCRF` code specific to cross-validation.
### Changed
- `pandas`, `fisher` and `statsmodels` dependencies are now optional.
- `gecco train` command expects a cluster table in addition to the feature
   table to know the types of the input BGCs.

## [v0.3.0] - 2020-08-03
[v0.3.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.2.2...v0.3.0
### Changed
- Replaced Nearest-Neighbours classifier with Random Forest to perform type
  prediction for candidate BGCs.
- `gecco.knn` module was renamed to implementation-agnostic name `gecco.types`.
### Fixed
- Extraction of domain composition taking a long time in `gecco train` command.
### Removed
- `--metric` argument to the `gecco run` CLI command.

## [v0.2.2] - 2020-07-31
[v0.2.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.2.1...v0.2.2
### Changed
- `Domain` and `Gene` can now carry qualifiers that are used when they
  are translated to a sequence feature.
### Added
- InterPro names, accessions, and HMMER e-value for each annotated domain
  in GenBank output files.

## [v0.2.1] - 2020-07-23
[v0.2.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.2.0...v0.2.1
### Fixed
- Various potential crashes in `ClusterRefiner` code.
### Removed
- Uneeded feature dictionary filtering in `ClusterCRF` for models with
  Fisher Exact Test feature selection.

## [v0.2.0] - 2020-07-23
[v0.2.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.1.1...v0.2.0
### Fixed
- `pandas` warning about unsorted columns in `gecco run`.
### Removed
- `Gene.probability` property, replaced by `Gene.maximum_probability` and
  `Gene.average_probability` properties to be explicit.
### Changed
- Internal model now uses `Pfam` and `Tigrfam` with the top 35% features
  selected with Fisher's Exact Test.
- `ClusterRefiner` now removes genes on `Cluster` edges if they do not
  contain any domain annotation.

## [v0.1.1] - 2020-07-22
[v0.1.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.1.0...v0.1.1
### Added
- `ClusterCRF.predict_probabilities` to annotate a list of `Gene`.
### Changed
- BGC probability is now stored at the `Domain` level instead of at the `Gene`
  level, independently of the feature extraction level used by the CRF.
- `ClusterKNN` will use the model path provided to `gecco run` if any.
### Docs
- Added this changelog file to document changes in the code.
- Added documentation to `gecco` submodules missing some.
- Included the `CHANGELOG.md` file to the generated docs.

## [v0.1.0] - 2020-07-17
[v0.1.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.0.1...v0.1.0
Initial release.

## [v0.0.1] - 2018-08-13
[v0.0.1]: https://git.embl.de/grp-zeller/GECCO/compare/37afb97...v0.0.1
Proof-of-concept.