Mercurial > repos > althonos > gecco
annotate CHANGELOG.md @ 19:cc91d730cc4f draft
Fix syntax of Galaxy script for GECCO
author | althonos |
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date | Mon, 16 Jan 2023 18:35:56 +0000 |
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1 # Changelog |
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2 All notable changes to this project will be documented in this file. |
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3 |
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4 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) |
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5 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). |
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6 |
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7 ## [Unreleased] |
19 | 8 [Unreleased]: https://github.com/zellerlab/GECCO/compare/v0.9.6...master |
9 | |
10 | |
11 ## [v0.9.6] - 2023-01-11 | |
12 [v0.9.6]: https://github.com/zellerlab/GECCO/compare/v0.9.5...v0.9.6 | |
13 | |
14 ### Added | |
15 - Gene Ontology annotations to `gecco.interpro` local metadata. | |
16 - Reference to Gene Ontology terms and derived functions to `gecco.model.Domain` objects. | |
17 - Gene color based on predicted function in `gecco.model.Gene.to_seq_feature`. | |
18 | |
19 ### Fixed | |
20 - Missing `gzip` import in the CLI preventing usage of gzip-compressed inputs. | |
21 - Invalid coordinates of domains found in reverse-strand genes. | |
22 - Detection of entry points with `importlib.metadata` on older Python versions. | |
23 | |
24 ### Changed | |
25 - `bgc_id` columns of cluster tables are renamed `cluster_id`. | |
26 - `gecco.model.ProductType` is renamed to `gecco.model.ClusterType`. | |
27 - Bumped `pyrodigal` dependency to `v2.0`. | |
28 - Bumped `pyhmmer` dependency to `v0.7`. | |
18 | 29 |
30 | |
31 ## [v0.9.5] - 2022-08-10 | |
19 | 32 [v0.9.5]: https://github.com/zellerlab/GECCO/compare/v0.9.4...v0.9.5 |
18 | 33 |
34 ### Added | |
35 - `gecco predict` command to predict BGCs from an annotated genome. | |
36 - `Protein.with_seq` function to assign a new sequence to a protein object. | |
37 | |
38 ### Fixed | |
39 - Issue with antiSMASH sideload JSON file generation in `gecco run` and `gecco predict`. | |
40 - Make `gecco.orf` handle STOP codons consistently ([#9](https://github.com/zellerlab/GECCO/issues/9)). | |
17 | 41 |
42 | |
43 ## [v0.9.4] - 2022-05-31 | |
19 | 44 [v0.9.4]: https://github.com/zellerlab/GECCO/compare/v0.9.3...v0.9.4 |
17 | 45 |
46 ### Added | |
47 - `classes_` property to `TypeClassifier` to access the `classes_` attribute of the `TypeBinarizer`. | |
48 - Alternative ORF finder `CDSFinder` which simply extracts CDS features from input sequences ([#8](https://github.com/zellerlab/GECCO/issues/8)). | |
49 - Support for annotating domains with "exclusive" HMMs to annotate genes with *at most* one HMM from the library. | |
50 | |
51 ### Changed | |
52 - `ProductType` is not restricted to MIBiG types anymore and can support any string as a base type identifier. | |
53 - `PyrodigalFinder` now uses `multiprocessing.pool.ThreadPool` instead of custom thread code thanks to `OrfFinder.find_genes` reentrancy introduced in Pyrodigal `v1.0`. | |
54 - `PyrodigalFinder` can now be used in single / non-meta mode from the API. | |
55 - BUmped minimum `rich` version to `12.3` to use `None` total in progress bars when the size of an HMM library is unknown. | |
56 | |
57 ### Fixed | |
58 - Broken MyPy type annotations in the `gecco.model` and `gecco.cli` modules. | |
16 | 59 |
60 | |
61 ## [v0.9.3] - 2022-05-13 | |
19 | 62 [v0.9.3]: https://github.com/zellerlab/GECCO/compare/v0.9.2...v0.9.3 |
16 | 63 |
64 ### Changed | |
65 - `--format` flag of `gecco annotate` and `gecco run` CLI commands is now made lowercase before giving value to `Bio.SeqIO`. | |
66 | |
67 ### Fixed | |
68 - Genes with duplicate IDs being silently ignored in `HMMER.run`. | |
69 | |
15 | 70 |
71 ## [v0.9.2] - 2022-04-11 | |
19 | 72 [v0.9.2]: https://github.com/zellerlab/GECCO/compare/v0.9.1...v0.9.2 |
15 | 73 |
74 ### Added | |
75 - Padding of short sequences with empty genes when predicting probabilities in `ClusterCRF`. | |
14 | 76 |
77 ## [v0.9.1] - 2022-04-05 | |
19 | 78 [v0.9.1]: https://github.com/zellerlab/GECCO/compare/v0.9.1-alpha4...v0.9.1 |
14 | 79 |
80 ### Changed | |
81 - Make the `genes.tsv` and `features.tsv` table contain all genes even when they come from a contig too short to be processed by the CRF sliding window. | |
82 - Replaced the `--force-clusters-tsv` flag with a `--force-tsv` flag to force writing TSV tables even when no genes or clusters were found in `gecco run` or `gecco annotate`. | |
13 | 83 |
84 ## [v0.9.1-alpha4] - 2022-03-31 | |
19 | 85 [v0.9.1-alpha4]: https://github.com/zellerlab/GECCO/compare/v0.9.1-alpha3...v0.9.1-alpha4 |
13 | 86 |
87 Retrain internal model with: | |
88 ``` | |
89 $ python -m gecco -vv train --c1 0.4 --c2 0 --select 0.25 --window-size 20 \ | |
90 -f mibig-2.0.proG2.Pfam-v35.0.features.tsv \ | |
91 -c mibig-2.0.proG2.clusters.tsv \ | |
14 | 92 -g GECCO-data/data/embeddings/mibig-2.0.proG2.genes.tsv \ |
13 | 93 -o models/v0.9.1-alpha4 |
94 ``` | |
12 | 95 |
96 ## [v0.9.1-alpha3] - 2022-03-23 | |
19 | 97 [v0.9.1-alpha3]: https://github.com/zellerlab/GECCO/compare/v0.9.1-alpha2...v0.9.1-alpha3 |
12 | 98 |
99 ### Added | |
100 - `gecco.model.GeneTable` class to store gene coordinates independently of protein domains. | |
101 | |
102 ### Changed | |
103 - Refactored implementation of `load` and `dump` methods for `Table` classes into a dedicated base class. | |
104 - `gecco run` and `gecco annotate` now output a gene table in addition to the feature and cluster tables. | |
105 - `gecco train` expects a gene table instead of a GFF file for the gene coordinates. | |
11 | 106 |
107 ## [v0.9.1-alpha2] - 2022-03-23 | |
19 | 108 [v0.9.1-alpha2]: https://github.com/zellerlab/GECCO/compare/v0.9.1-alpha1...v0.9.1-alpha2 |
11 | 109 |
110 ### Fixed | |
111 - `TypeClassifier.trained` not being able to read unknown types from type tables. | |
10 | 112 |
113 ## [v0.9.1-alpha1] - 2022-03-20 | |
19 | 114 [v0.9.1-alpha1]: https://github.com/zellerlab/GECCO/compare/v0.8.10...v0.9.1-alpha1 |
10 | 115 Candidate release with support for a sliding window in the CRF prediction algorithm. |
9 | 116 |
117 ## [v0.8.10] - 2022-02-23 | |
19 | 118 [v0.8.10]: https://github.com/zellerlab/GECCO/compare/v0.8.9...v0.8.10 |
9 | 119 ### Fixed |
120 - `--antismash-sideload` flag of `gecco run` causing command to crash. | |
8 | 121 |
122 ## [v0.8.9] - 2022-02-22 | |
19 | 123 [v0.8.9]: https://github.com/zellerlab/GECCO/compare/v0.8.8...v0.8.9 |
8 | 124 ### Removed |
125 - Prediction and support for the *Other* biosynthetic type of MIBiG clusters. | |
7 | 126 |
127 ## [v0.8.8] - 2022-02-21 | |
19 | 128 [v0.8.8]: https://github.com/zellerlab/GECCO/compare/v0.8.7...v0.8.8 |
7 | 129 ### Fixed |
130 - `ClusterRefiner` filtering method for edge genes not working as intended. | |
131 - `gecco run` and `gecco annotate` commands crashing on missing input files instead of nicely rendering the error. | |
5 | 132 |
6 | 133 ## [v0.8.7] - 2022-02-18 |
19 | 134 [v0.8.7]: https://github.com/zellerlab/GECCO/compare/v0.8.6...v0.8.7 |
6 | 135 ### Fixed |
136 - `interpro.json` metadata file not being included in distribution files. | |
137 - Missing docstring for `Protein.with_domains` method. | |
138 ### Changed | |
139 - Bump minimum `scikit-learn` version to `v1.0` for Python3.7+. | |
140 | |
141 ## [v0.8.6] - 2022-02-17 - YANKED | |
19 | 142 [v0.8.6]: https://github.com/zellerlab/GECCO/compare/v0.8.5...v0.8.6 |
5 | 143 ### Added |
144 - CLI flag for enabling region masking for contigs processed by Prodigal. | |
145 - CLI flag for controlling region distance used for edge distance filtering. | |
146 ### Changed | |
147 - `gecco.model.Gene` and `gecco.model.Protein` are now immutable data classes. | |
148 - Bump minimum `pyrodigal` version to `v0.6.4` to use region masking. | |
149 - Implement filtering for extracted clusters based on distance to the contig edge. | |
150 - Store InterPro metadata file uncompressed for version-control integration. | |
151 ### Fixed | |
152 - Mark `BGC0000930` as `Terpene` in the type classifier data. | |
153 - Progress bar messages are now in consistent format. | |
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154 |
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155 ## [v0.8.5] - 2021-11-21 |
19 | 156 [v0.8.5]: https://github.com/zellerlab/GECCO/compare/v0.8.4...v0.8.5 |
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157 ### Added |
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158 - Minimal compatibility support for running GECCO inside of Galaxy workflows. |
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159 |
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160 ## [v0.8.4] - 2021-09-26 |
19 | 161 [v0.8.4]: https://github.com/zellerlab/GECCO/compare/v0.8.3-post1...v0.8.4 |
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162 ### Fixed |
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163 - `gecco convert gbk --format bigslice` failing to run because of outdated code ([#5](https://github.com/zellerlab/GECCO/issues/5)). |
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164 - `gecco convert gbk --format bigslice` not creating files with names conforming to BiG-SLiCE expected input. |
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165 ### Changed |
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166 - Bump minimum `pyrodigal` version to `v0.6.2` to use platform-accelerated code if supported. |
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167 |
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168 ## [v0.8.3-post1] - 2021-08-23 |
19 | 169 [v0.8.3-post1]: https://github.com/zellerlab/GECCO/compare/v0.8.3...v0.8.3-post1 |
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170 ### Fixed |
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171 - Wrong default value for `--threshold` being shown in `gecco run` help message. |
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172 |
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173 ## [v0.8.3] - 2021-08-23 |
19 | 174 [v0.8.3]: https://github.com/zellerlab/GECCO/compare/v0.8.2...v0.8.3 |
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175 ### Changed |
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176 - Default probability threshold for segmentation to 0.3 (from 0.4). |
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177 |
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178 ## [v0.8.2] - 2021-07-31 |
19 | 179 [v0.8.2]: https://github.com/zellerlab/GECCO/compare/v0.8.1...v0.8.2 |
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180 ### Fixed |
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181 - `gecco run` crashing on Python 3.6 because of missing `contextlib.nullcontext` class. |
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182 ### Changed |
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183 - `gecco run` and `gecco annotate` will not try to count the number of profiles when given an external HMM file with the `--hmm` flag. |
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184 - `PyHMMER.run` now reports the *p-value* of each domain in addition to the *e-value* as a `/note` qualifier. |
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185 |
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186 ## [v0.8.1] - 2021-07-29 |
19 | 187 [v0.8.1]: https://github.com/zellerlab/GECCO/compare/v0.8.0...v0.8.1 |
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188 ### Changed |
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189 - `gecco run` now filters out unneeded features before annotating, making it easier to analyze the results of a run with a custom `--model`. |
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190 ### Fixed |
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191 - `gecco` reporting about using Pfam `v33.1` while actually using `v34.0` because of an outdated field in `gecco/hmmer/Pfam.ini`. |
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192 ### Added |
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193 - Missing documentation for the `strand` attribute of `gecco.model.Gene`. |
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194 |
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195 ## [v0.8.0] - 2021-07-03 |
19 | 196 [v0.8.0]: https://github.com/zellerlab/GECCO/compare/v0.7.0...v0.8.0 |
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197 ### Changed |
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198 - Retrain internal model using new sequence embeddings and remove broken/duplicate BGCs from MIBiG 2.0. |
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199 - Bump minimum `pyhmmer` version to `v0.4.0` to improve exception handling. |
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200 - Bump minimum `pyrodigal` version to `v0.5.0` to fix sequence decoding on some platforms. |
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201 - Use p-values instead of e-values to filter domains obtained with HMMER. |
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202 - `gecco cv` and `gecco train` now seed the RNG with a user-defined seed before shuffling rows of training data. |
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203 ### Fixed |
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204 - Extraction of BGC compositions for the type predictor while training. |
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205 - `ClusterCRF.trained` failing to open an external model. |
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206 ### Added |
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207 - `Domain.pvalue` attribute to access the p-value of a domain annotation. |
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208 - Mandatory `pvalue` column to `FeatureTable` objects. |
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209 - Support for loading several feature tables in `gecco train` and `gecco cv`. |
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210 - Warnings to `ClusterCRF.fit` when selecting uninformative features. |
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211 - `--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. |
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212 ### Removed |
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213 - Outdated `gecco embed` command. |
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214 - Unused `--truncate` flag from the `gecco train` CLI. |
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215 - Tigrfam domains, which is not improving performance on the new training data. |
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216 |
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217 ## [v0.7.0] - 2021-05-31 |
19 | 218 [v0.7.0]: https://github.com/zellerlab/GECCO/compare/v0.6.3...v0.7.0 |
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219 ### Added |
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220 - Support for writing an AntiSMASH sideload JSON file after a `gecco run` workflow. |
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221 - Code for converting GenBank files in BiG-SLiCE compatible format with the `gecco convert` subcommand. |
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222 - Documentation about using GECCO in combination with AntiSMASH or BiG-SLiCE. |
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223 ### Changed |
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224 - Minimum Biopython version to `v1.73` for compatibility with older bioinformatics tooling. |
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225 - Internal domain composition shipped in the `gecco.types` with newer composition array obtained directly from MIBiG files. |
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226 ### Removed |
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227 - Outdated notice about `-vvv` verbosity level in the help message of the main `gecco` command. |
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228 |
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229 ## [v0.6.3] - 2021-05-10 |
19 | 230 [v0.6.3]: https://github.com/zellerlab/GECCO/compare/v0.6.2...v0.6.3 |
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231 ### Fixed |
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232 - HMMER annotation not properly handling inputs with multiple contigs. |
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233 - Some progress bar totals displaying as floats in the CLI. |
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234 ### Changed |
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235 - `PyHMMER` now sets the `Z` and `domZ` values from the number of proteins given to the search pipeline. |
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236 - `gecco.cli` delegates imports to make CLI more responsive. |
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237 - `pkg_resources` has been replaced with `importlib.resources` and `importlib.metadata` where applicable. |
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238 - `multiprocessing.cpu_count` has been replaced with `os.cpu_count` where applicable. |
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239 |
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240 ## [v0.6.2] - 2021-05-04 |
19 | 241 [v0.6.2]: https://github.com/zellerlab/GECCO/compare/v0.6.1...v0.6.2 |
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242 ### Fixed |
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243 - `gecco cv loto` crashing because of outdated code. |
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244 ### Changed |
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245 - Logging-style prompt will only display if GECCO is running with `-vv` flag. |
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246 ### Added |
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247 - GECCO bioRxiv paper reference to `Cluster.to_seq_record` output record. |
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248 |
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249 ## [v0.6.1] - 2021-03-15 |
19 | 250 [v0.6.1]: https://github.com/zellerlab/GECCO/compare/v0.6.0...v0.6.1 |
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251 ### Fixed |
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252 - Progress bar not being disabled by `-q` flag in CLI. |
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253 - Fallback to using HMM name if accession is not available in `PyHMMER`. |
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254 - Group genes by source contig and process them separately in `PyHMMER` to avoid bogus E-values. |
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255 ### Added |
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256 - `psutil` dependency to get the number of physical CPU cores on the host machine. |
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257 - Support for using an arbitrary mapping of positives to negatives in `gecco embed`. |
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258 ### Removed |
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259 - Unused and outdated `HMMER` and `DomainRow` classes from `gecco.hmmer`. |
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260 |
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261 ## [v0.6.0] - 2021-02-28 |
19 | 262 [v0.6.0]: https://github.com/zellerlab/GECCO/compare/v0.5.5...v0.6.0 |
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263 ### Changed |
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264 - Updated internal model with a cleaned-up version of the MIBiG-2.0 |
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265 Pfam-33.1/Tigrfam-15.0 embedding. |
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266 - Updated internal InterPro catalog. |
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267 ### Fixed |
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268 - Features not being grouped together in `gecco cv` and `gecco train` |
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269 when provided with a feature table where rows were not sorted by |
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270 protein IDs. |
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271 |
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272 ## [v0.5.5] - 2021-02-28 |
19 | 273 [v0.5.5]: https://github.com/zellerlab/GECCO/compare/v0.5.4...v0.5.5 |
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274 ### Fixed |
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275 - `gecco cv` bug causing only the last fold to be written. |
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276 |
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277 ## [v0.5.4] - 2021-02-28 |
19 | 278 [v0.5.4]: https://github.com/zellerlab/GECCO/compare/v0.5.3...v0.5.4 |
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279 ### Changed |
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280 - Replaced `verboselogs`, `coloredlogs` and `better-exceptions` with `rich`. |
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281 ### Removed |
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282 - `tqdm` training dependency. |
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283 ### Added |
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284 - `gecco annotate` command to produce a feature table from a genomic file. |
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285 - `gecco embed` to embed BGCs into non-BGC regions using feature tables. |
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286 |
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287 ## [v0.5.3] - 2021-02-21 |
19 | 288 [v0.5.3]: https://github.com/zellerlab/GECCO/compare/v0.5.2...v0.5.3 |
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289 ### Fixed |
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290 - Coordinates of genes in output GenBank files. |
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291 - Potential issue with the number of CPUs in `PyHMMER.run`. |
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292 ### Changed |
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293 - Bump required `pyrodigal` version to `v0.4.2` to fix buffer overflow. |
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294 |
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295 ## [v0.5.2] - 2021-01-29 |
19 | 296 [v0.5.2]: https://github.com/zellerlab/GECCO/compare/v0.5.1...v0.5.2 |
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297 ### Added |
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298 - Support for downloading HMM files directly from GitHub releases assets. |
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299 - Validation of filtered HMMs with MD5 checksum. |
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300 ### Fixed |
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301 - Invalid coordinates of protein domains in GenBank output files. |
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302 - `gecco.interpro` module not being added to wheel distribution. |
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303 ### Changed |
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304 - Bump required `pyhmmer` version to `v0.2.1`. |
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305 |
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306 ## [v0.5.1] - 2021-01-15 |
19 | 307 [v0.5.1]: https://github.com/zellerlab/GECCO/compare/v0.5.0...v0.5.1 |
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308 ### Fixed |
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309 - `--hmm` flag being ignored in in `gecco run` command. |
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310 - `PyHMMER` using HMM names instead of accessions, causing issues with Pfam HMMs. |
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311 |
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312 ## [v0.5.0] - 2021-01-11 |
19 | 313 [v0.5.0]: https://github.com/zellerlab/GECCO/compare/v0.4.5...v0.5.0 |
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314 ### Added |
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315 - Explicit support for Python 3.9. |
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316 ### Changed |
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317 - [`pyhmmer`](https://pypi.org/project/pyhmmer) is used to annotate protein sequences instead of HMMER3 binary `hmmsearch`. |
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318 - HMM files are stored in binary format to speedup parsing and reduce storage size. |
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319 - `tqdm` is now a *training*-only dependency. |
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320 - `gecco cv` now requires *training* dependencies. |
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321 |
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322 ## [v0.4.5] - 2020-11-23 |
19 | 323 [v0.4.5]: https://github.com/zellerlab/GECCO/compare/v0.4.4...v0.4.5 |
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324 ### Added |
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325 - Additional `fold` column to cross-validation table output. |
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326 ### Changed |
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327 - Use sequence ID instead of protein ID to extract type from cluster in `gecco cv`. |
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328 - Install HMM data in pre-pressed format to make `hmmsearch` runs faster on short sequences. |
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329 - `gecco.orf` was rewritten to extract genes from input sequences in parallel. |
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330 |
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331 ## [v0.4.4] - 2020-09-30 |
19 | 332 [v0.4.4]: https://github.com/zellerlab/GECCO/compare/v0.4.3...v0.4.4 |
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333 ### Added |
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334 - `gecco cv loto` command to run LOTO cross-validation using BGC types |
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335 for stratification. |
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336 - `header` keyword argument to `FeatureTable.dump` and `ClusterTable.dump` |
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337 to write the table without the column header allowing to append to an |
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338 existing table. |
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339 - `__getitem__` implementation for `FeatureTable` and `ClusterTable` |
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340 that returns a single row or a sub-table from a table. |
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341 ### Fixed |
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342 - `gecco cv` command now writes results iteratively instead of holding |
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343 the tables for every fold in memory. |
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344 ### Changed |
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345 - Bumped `pandas` training dependency to `v1.0`. |
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346 |
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347 ## [v0.4.3] - 2020-09-07 |
19 | 348 [v0.4.3]: https://github.com/zellerlab/GECCO/compare/v0.4.2...v0.4.3 |
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349 ### Fixed |
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350 - GenBank files being written with invalid `/cds` feature type. |
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351 ### Changed |
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352 - Blocked installation of Biopython `v1.78` or newer as it removes `Bio.Alphabet` |
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353 and breaks the current code. |
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354 |
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355 ## [v0.4.2] - 2020-08-07 |
19 | 356 [v0.4.2]: https://github.com/zellerlab/GECCO/compare/v0.4.1...v0.4.2 |
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357 ### Fixed |
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358 - `TypeClassifier.predict_types` using inverse type probabilities when |
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359 given several clusters to process. |
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360 |
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361 ## [v0.4.1] - 2020-08-07 |
19 | 362 [v0.4.1]: https://github.com/zellerlab/GECCO/compare/v0.4.0...v0.4.1 |
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363 ### Fixed |
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364 - `gecco run` command crashing on input sequences not containing any genes. |
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365 |
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366 ## [v0.4.0] - 2020-08-06 |
19 | 367 [v0.4.0]: https://github.com/zellerlab/GECCO/compare/v0.3.0...v0.4.0 |
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368 ### Added |
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369 - `gecco.model.ProductType` enum to model the biosynthetic class of a BGC. |
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370 ### Removed |
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371 - `pandas` interaction from internal data model. |
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372 - `ClusterCRF` code specific to cross-validation. |
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373 ### Changed |
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374 - `pandas`, `fisher` and `statsmodels` dependencies are now optional. |
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375 - `gecco train` command expects a cluster table in addition to the feature |
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376 table to know the types of the input BGCs. |
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377 |
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378 ## [v0.3.0] - 2020-08-03 |
19 | 379 [v0.3.0]: https://github.com/zellerlab/GECCO/compare/v0.2.2...v0.3.0 |
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380 ### Changed |
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381 - Replaced Nearest-Neighbours classifier with Random Forest to perform type |
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382 prediction for candidate BGCs. |
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383 - `gecco.knn` module was renamed to implementation-agnostic name `gecco.types`. |
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384 ### Fixed |
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385 - Extraction of domain composition taking a long time in `gecco train` command. |
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386 ### Removed |
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387 - `--metric` argument to the `gecco run` CLI command. |
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388 |
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389 ## [v0.2.2] - 2020-07-31 |
19 | 390 [v0.2.2]: https://github.com/zellerlab/GECCO/compare/v0.2.1...v0.2.2 |
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391 ### Changed |
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392 - `Domain` and `Gene` can now carry qualifiers that are used when they |
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393 are translated to a sequence feature. |
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394 ### Added |
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395 - InterPro names, accessions, and HMMER e-value for each annotated domain |
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396 in GenBank output files. |
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397 |
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398 ## [v0.2.1] - 2020-07-23 |
19 | 399 [v0.2.1]: https://github.com/zellerlab/GECCO/compare/v0.2.0...v0.2.1 |
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400 ### Fixed |
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401 - Various potential crashes in `ClusterRefiner` code. |
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402 ### Removed |
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403 - Uneeded feature dictionary filtering in `ClusterCRF` for models with |
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404 Fisher Exact Test feature selection. |
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405 |
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406 ## [v0.2.0] - 2020-07-23 |
19 | 407 [v0.2.0]: https://github.com/zellerlab/GECCO/compare/v0.1.1...v0.2.0 |
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408 ### Fixed |
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409 - `pandas` warning about unsorted columns in `gecco run`. |
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410 ### Removed |
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411 - `Gene.probability` property, replaced by `Gene.maximum_probability` and |
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412 `Gene.average_probability` properties to be explicit. |
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413 ### Changed |
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414 - Internal model now uses `Pfam` and `Tigrfam` with the top 35% features |
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415 selected with Fisher's Exact Test. |
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416 - `ClusterRefiner` now removes genes on `Cluster` edges if they do not |
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417 contain any domain annotation. |
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418 |
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419 ## [v0.1.1] - 2020-07-22 |
19 | 420 [v0.1.1]: https://github.com/zellerlab/GECCO/compare/v0.1.0...v0.1.1 |
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421 ### Added |
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422 - `ClusterCRF.predict_probabilities` to annotate a list of `Gene`. |
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423 ### Changed |
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424 - BGC probability is now stored at the `Domain` level instead of at the `Gene` |
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425 level, independently of the feature extraction level used by the CRF. |
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426 - `ClusterKNN` will use the model path provided to `gecco run` if any. |
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427 ### Docs |
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428 - Added this changelog file to document changes in the code. |
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429 - Added documentation to `gecco` submodules missing some. |
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430 - Included the `CHANGELOG.md` file to the generated docs. |
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431 |
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432 ## [v0.1.0] - 2020-07-17 |
19 | 433 [v0.1.0]: https://github.com/zellerlab/GECCO/compare/v0.0.1...v0.1.0 |
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434 Initial release. |
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435 |
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436 ## [v0.0.1] - 2018-08-13 |
19 | 437 [v0.0.1]: https://github.com/zellerlab/GECCO/compare/37afb97...v0.0.1 |
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438 Proof-of-concept. |