Mercurial > repos > althonos > gecco
annotate CHANGELOG.md @ 21:6ba37b7dea42 draft
Release v0.9.7
author | althonos |
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date | Fri, 26 May 2023 12:10:43 +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] |
21 | 8 [Unreleased]: https://github.com/zellerlab/GECCO/compare/v0.9.7...master |
9 | |
10 | |
11 ## [v0.9.7] - 2023-05-26 | |
12 [v0.9.7]: https://github.com/zellerlab/GECCO/compare/v0.9.6...v0.9.7 | |
13 | |
14 ### Added | |
15 - Command line option to annotate proteins using bitscore cutoffs from HMMs. | |
16 - Command line option to disentangle overlapping domains after HMM annotation. | |
17 | |
18 ### Changed | |
19 - Bump `pyhmmer` dependency to `v0.8.0`. | |
20 - Bump `pyrodigal` dependency to `v2.1.0`. | |
21 - Rewrite `gecco.model` to use `polars` for managing tabular data. | |
22 - Replace `pandas` dependencies with `polars` | |
23 - Update `gecco run` to skip type classification for tasks without an assigned cluster type. | |
24 | |
25 ### Fixed | |
26 - `Cluster.to_seq_record` crashing when called on a cluster with `types` attribute unset. | |
27 - Progress bar resetting when performing domain annotation with multiple HMMs. | |
28 | |
29 ### Removed | |
30 - Support for Python 3.7. | |
19 | 31 |
32 | |
33 ## [v0.9.6] - 2023-01-11 | |
34 [v0.9.6]: https://github.com/zellerlab/GECCO/compare/v0.9.5...v0.9.6 | |
35 | |
36 ### Added | |
37 - Gene Ontology annotations to `gecco.interpro` local metadata. | |
38 - Reference to Gene Ontology terms and derived functions to `gecco.model.Domain` objects. | |
39 - Gene color based on predicted function in `gecco.model.Gene.to_seq_feature`. | |
40 | |
41 ### Fixed | |
42 - Missing `gzip` import in the CLI preventing usage of gzip-compressed inputs. | |
43 - Invalid coordinates of domains found in reverse-strand genes. | |
44 - Detection of entry points with `importlib.metadata` on older Python versions. | |
45 | |
46 ### Changed | |
47 - `bgc_id` columns of cluster tables are renamed `cluster_id`. | |
48 - `gecco.model.ProductType` is renamed to `gecco.model.ClusterType`. | |
49 - Bumped `pyrodigal` dependency to `v2.0`. | |
50 - Bumped `pyhmmer` dependency to `v0.7`. | |
18 | 51 |
52 | |
53 ## [v0.9.5] - 2022-08-10 | |
19 | 54 [v0.9.5]: https://github.com/zellerlab/GECCO/compare/v0.9.4...v0.9.5 |
18 | 55 |
56 ### Added | |
57 - `gecco predict` command to predict BGCs from an annotated genome. | |
58 - `Protein.with_seq` function to assign a new sequence to a protein object. | |
59 | |
60 ### Fixed | |
61 - Issue with antiSMASH sideload JSON file generation in `gecco run` and `gecco predict`. | |
62 - Make `gecco.orf` handle STOP codons consistently ([#9](https://github.com/zellerlab/GECCO/issues/9)). | |
17 | 63 |
64 | |
65 ## [v0.9.4] - 2022-05-31 | |
19 | 66 [v0.9.4]: https://github.com/zellerlab/GECCO/compare/v0.9.3...v0.9.4 |
17 | 67 |
68 ### Added | |
69 - `classes_` property to `TypeClassifier` to access the `classes_` attribute of the `TypeBinarizer`. | |
70 - Alternative ORF finder `CDSFinder` which simply extracts CDS features from input sequences ([#8](https://github.com/zellerlab/GECCO/issues/8)). | |
71 - Support for annotating domains with "exclusive" HMMs to annotate genes with *at most* one HMM from the library. | |
72 | |
73 ### Changed | |
74 - `ProductType` is not restricted to MIBiG types anymore and can support any string as a base type identifier. | |
75 - `PyrodigalFinder` now uses `multiprocessing.pool.ThreadPool` instead of custom thread code thanks to `OrfFinder.find_genes` reentrancy introduced in Pyrodigal `v1.0`. | |
76 - `PyrodigalFinder` can now be used in single / non-meta mode from the API. | |
77 - BUmped minimum `rich` version to `12.3` to use `None` total in progress bars when the size of an HMM library is unknown. | |
78 | |
79 ### Fixed | |
80 - Broken MyPy type annotations in the `gecco.model` and `gecco.cli` modules. | |
16 | 81 |
82 | |
83 ## [v0.9.3] - 2022-05-13 | |
19 | 84 [v0.9.3]: https://github.com/zellerlab/GECCO/compare/v0.9.2...v0.9.3 |
16 | 85 |
86 ### Changed | |
87 - `--format` flag of `gecco annotate` and `gecco run` CLI commands is now made lowercase before giving value to `Bio.SeqIO`. | |
88 | |
89 ### Fixed | |
90 - Genes with duplicate IDs being silently ignored in `HMMER.run`. | |
91 | |
15 | 92 |
93 ## [v0.9.2] - 2022-04-11 | |
19 | 94 [v0.9.2]: https://github.com/zellerlab/GECCO/compare/v0.9.1...v0.9.2 |
15 | 95 |
96 ### Added | |
97 - Padding of short sequences with empty genes when predicting probabilities in `ClusterCRF`. | |
14 | 98 |
99 ## [v0.9.1] - 2022-04-05 | |
19 | 100 [v0.9.1]: https://github.com/zellerlab/GECCO/compare/v0.9.1-alpha4...v0.9.1 |
14 | 101 |
102 ### Changed | |
103 - 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. | |
104 - 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 | 105 |
106 ## [v0.9.1-alpha4] - 2022-03-31 | |
19 | 107 [v0.9.1-alpha4]: https://github.com/zellerlab/GECCO/compare/v0.9.1-alpha3...v0.9.1-alpha4 |
13 | 108 |
109 Retrain internal model with: | |
110 ``` | |
111 $ python -m gecco -vv train --c1 0.4 --c2 0 --select 0.25 --window-size 20 \ | |
112 -f mibig-2.0.proG2.Pfam-v35.0.features.tsv \ | |
113 -c mibig-2.0.proG2.clusters.tsv \ | |
14 | 114 -g GECCO-data/data/embeddings/mibig-2.0.proG2.genes.tsv \ |
13 | 115 -o models/v0.9.1-alpha4 |
116 ``` | |
12 | 117 |
118 ## [v0.9.1-alpha3] - 2022-03-23 | |
19 | 119 [v0.9.1-alpha3]: https://github.com/zellerlab/GECCO/compare/v0.9.1-alpha2...v0.9.1-alpha3 |
12 | 120 |
121 ### Added | |
122 - `gecco.model.GeneTable` class to store gene coordinates independently of protein domains. | |
123 | |
124 ### Changed | |
125 - Refactored implementation of `load` and `dump` methods for `Table` classes into a dedicated base class. | |
126 - `gecco run` and `gecco annotate` now output a gene table in addition to the feature and cluster tables. | |
127 - `gecco train` expects a gene table instead of a GFF file for the gene coordinates. | |
11 | 128 |
129 ## [v0.9.1-alpha2] - 2022-03-23 | |
19 | 130 [v0.9.1-alpha2]: https://github.com/zellerlab/GECCO/compare/v0.9.1-alpha1...v0.9.1-alpha2 |
11 | 131 |
132 ### Fixed | |
133 - `TypeClassifier.trained` not being able to read unknown types from type tables. | |
10 | 134 |
135 ## [v0.9.1-alpha1] - 2022-03-20 | |
19 | 136 [v0.9.1-alpha1]: https://github.com/zellerlab/GECCO/compare/v0.8.10...v0.9.1-alpha1 |
10 | 137 Candidate release with support for a sliding window in the CRF prediction algorithm. |
9 | 138 |
139 ## [v0.8.10] - 2022-02-23 | |
19 | 140 [v0.8.10]: https://github.com/zellerlab/GECCO/compare/v0.8.9...v0.8.10 |
9 | 141 ### Fixed |
142 - `--antismash-sideload` flag of `gecco run` causing command to crash. | |
8 | 143 |
144 ## [v0.8.9] - 2022-02-22 | |
19 | 145 [v0.8.9]: https://github.com/zellerlab/GECCO/compare/v0.8.8...v0.8.9 |
8 | 146 ### Removed |
147 - Prediction and support for the *Other* biosynthetic type of MIBiG clusters. | |
7 | 148 |
149 ## [v0.8.8] - 2022-02-21 | |
19 | 150 [v0.8.8]: https://github.com/zellerlab/GECCO/compare/v0.8.7...v0.8.8 |
7 | 151 ### Fixed |
152 - `ClusterRefiner` filtering method for edge genes not working as intended. | |
153 - `gecco run` and `gecco annotate` commands crashing on missing input files instead of nicely rendering the error. | |
5 | 154 |
6 | 155 ## [v0.8.7] - 2022-02-18 |
19 | 156 [v0.8.7]: https://github.com/zellerlab/GECCO/compare/v0.8.6...v0.8.7 |
6 | 157 ### Fixed |
158 - `interpro.json` metadata file not being included in distribution files. | |
159 - Missing docstring for `Protein.with_domains` method. | |
160 ### Changed | |
161 - Bump minimum `scikit-learn` version to `v1.0` for Python3.7+. | |
162 | |
163 ## [v0.8.6] - 2022-02-17 - YANKED | |
19 | 164 [v0.8.6]: https://github.com/zellerlab/GECCO/compare/v0.8.5...v0.8.6 |
5 | 165 ### Added |
166 - CLI flag for enabling region masking for contigs processed by Prodigal. | |
167 - CLI flag for controlling region distance used for edge distance filtering. | |
168 ### Changed | |
169 - `gecco.model.Gene` and `gecco.model.Protein` are now immutable data classes. | |
170 - Bump minimum `pyrodigal` version to `v0.6.4` to use region masking. | |
171 - Implement filtering for extracted clusters based on distance to the contig edge. | |
172 - Store InterPro metadata file uncompressed for version-control integration. | |
173 ### Fixed | |
174 - Mark `BGC0000930` as `Terpene` in the type classifier data. | |
175 - Progress bar messages are now in consistent format. | |
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176 |
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177 ## [v0.8.5] - 2021-11-21 |
19 | 178 [v0.8.5]: https://github.com/zellerlab/GECCO/compare/v0.8.4...v0.8.5 |
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179 ### Added |
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180 - Minimal compatibility support for running GECCO inside of Galaxy workflows. |
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181 |
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182 ## [v0.8.4] - 2021-09-26 |
19 | 183 [v0.8.4]: https://github.com/zellerlab/GECCO/compare/v0.8.3-post1...v0.8.4 |
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184 ### Fixed |
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185 - `gecco convert gbk --format bigslice` failing to run because of outdated code ([#5](https://github.com/zellerlab/GECCO/issues/5)). |
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186 - `gecco convert gbk --format bigslice` not creating files with names conforming to BiG-SLiCE expected input. |
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187 ### Changed |
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188 - Bump minimum `pyrodigal` version to `v0.6.2` to use platform-accelerated code if supported. |
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189 |
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190 ## [v0.8.3-post1] - 2021-08-23 |
19 | 191 [v0.8.3-post1]: https://github.com/zellerlab/GECCO/compare/v0.8.3...v0.8.3-post1 |
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192 ### Fixed |
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193 - Wrong default value for `--threshold` being shown in `gecco run` help message. |
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194 |
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195 ## [v0.8.3] - 2021-08-23 |
19 | 196 [v0.8.3]: https://github.com/zellerlab/GECCO/compare/v0.8.2...v0.8.3 |
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197 ### Changed |
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198 - Default probability threshold for segmentation to 0.3 (from 0.4). |
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199 |
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200 ## [v0.8.2] - 2021-07-31 |
19 | 201 [v0.8.2]: https://github.com/zellerlab/GECCO/compare/v0.8.1...v0.8.2 |
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202 ### Fixed |
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203 - `gecco run` crashing on Python 3.6 because of missing `contextlib.nullcontext` class. |
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204 ### Changed |
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205 - `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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206 - `PyHMMER.run` now reports the *p-value* of each domain in addition to the *e-value* as a `/note` qualifier. |
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207 |
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208 ## [v0.8.1] - 2021-07-29 |
19 | 209 [v0.8.1]: https://github.com/zellerlab/GECCO/compare/v0.8.0...v0.8.1 |
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210 ### Changed |
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211 - `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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212 ### Fixed |
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213 - `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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214 ### Added |
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215 - Missing documentation for the `strand` attribute of `gecco.model.Gene`. |
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216 |
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217 ## [v0.8.0] - 2021-07-03 |
19 | 218 [v0.8.0]: https://github.com/zellerlab/GECCO/compare/v0.7.0...v0.8.0 |
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219 ### Changed |
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220 - Retrain internal model using new sequence embeddings and remove broken/duplicate BGCs from MIBiG 2.0. |
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221 - Bump minimum `pyhmmer` version to `v0.4.0` to improve exception handling. |
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222 - Bump minimum `pyrodigal` version to `v0.5.0` to fix sequence decoding on some platforms. |
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223 - Use p-values instead of e-values to filter domains obtained with HMMER. |
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224 - `gecco cv` and `gecco train` now seed the RNG with a user-defined seed before shuffling rows of training data. |
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225 ### Fixed |
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226 - Extraction of BGC compositions for the type predictor while training. |
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227 - `ClusterCRF.trained` failing to open an external model. |
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228 ### Added |
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229 - `Domain.pvalue` attribute to access the p-value of a domain annotation. |
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230 - Mandatory `pvalue` column to `FeatureTable` objects. |
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231 - Support for loading several feature tables in `gecco train` and `gecco cv`. |
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232 - Warnings to `ClusterCRF.fit` when selecting uninformative features. |
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233 - `--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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234 ### Removed |
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235 - Outdated `gecco embed` command. |
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236 - Unused `--truncate` flag from the `gecco train` CLI. |
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237 - Tigrfam domains, which is not improving performance on the new training data. |
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238 |
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239 ## [v0.7.0] - 2021-05-31 |
19 | 240 [v0.7.0]: https://github.com/zellerlab/GECCO/compare/v0.6.3...v0.7.0 |
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241 ### Added |
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242 - Support for writing an AntiSMASH sideload JSON file after a `gecco run` workflow. |
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243 - Code for converting GenBank files in BiG-SLiCE compatible format with the `gecco convert` subcommand. |
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244 - Documentation about using GECCO in combination with AntiSMASH or BiG-SLiCE. |
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245 ### Changed |
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246 - Minimum Biopython version to `v1.73` for compatibility with older bioinformatics tooling. |
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247 - Internal domain composition shipped in the `gecco.types` with newer composition array obtained directly from MIBiG files. |
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248 ### Removed |
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249 - Outdated notice about `-vvv` verbosity level in the help message of the main `gecco` command. |
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250 |
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251 ## [v0.6.3] - 2021-05-10 |
19 | 252 [v0.6.3]: https://github.com/zellerlab/GECCO/compare/v0.6.2...v0.6.3 |
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253 ### Fixed |
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254 - HMMER annotation not properly handling inputs with multiple contigs. |
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255 - Some progress bar totals displaying as floats in the CLI. |
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256 ### Changed |
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257 - `PyHMMER` now sets the `Z` and `domZ` values from the number of proteins given to the search pipeline. |
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258 - `gecco.cli` delegates imports to make CLI more responsive. |
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259 - `pkg_resources` has been replaced with `importlib.resources` and `importlib.metadata` where applicable. |
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260 - `multiprocessing.cpu_count` has been replaced with `os.cpu_count` where applicable. |
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261 |
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262 ## [v0.6.2] - 2021-05-04 |
19 | 263 [v0.6.2]: https://github.com/zellerlab/GECCO/compare/v0.6.1...v0.6.2 |
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264 ### Fixed |
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265 - `gecco cv loto` crashing because of outdated code. |
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266 ### Changed |
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267 - Logging-style prompt will only display if GECCO is running with `-vv` flag. |
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268 ### Added |
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269 - GECCO bioRxiv paper reference to `Cluster.to_seq_record` output record. |
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270 |
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271 ## [v0.6.1] - 2021-03-15 |
19 | 272 [v0.6.1]: https://github.com/zellerlab/GECCO/compare/v0.6.0...v0.6.1 |
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273 ### Fixed |
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274 - Progress bar not being disabled by `-q` flag in CLI. |
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275 - Fallback to using HMM name if accession is not available in `PyHMMER`. |
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276 - Group genes by source contig and process them separately in `PyHMMER` to avoid bogus E-values. |
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277 ### Added |
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278 - `psutil` dependency to get the number of physical CPU cores on the host machine. |
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279 - Support for using an arbitrary mapping of positives to negatives in `gecco embed`. |
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280 ### Removed |
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281 - Unused and outdated `HMMER` and `DomainRow` classes from `gecco.hmmer`. |
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282 |
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283 ## [v0.6.0] - 2021-02-28 |
19 | 284 [v0.6.0]: https://github.com/zellerlab/GECCO/compare/v0.5.5...v0.6.0 |
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285 ### Changed |
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286 - Updated internal model with a cleaned-up version of the MIBiG-2.0 |
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287 Pfam-33.1/Tigrfam-15.0 embedding. |
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288 - Updated internal InterPro catalog. |
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289 ### Fixed |
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290 - Features not being grouped together in `gecco cv` and `gecco train` |
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291 when provided with a feature table where rows were not sorted by |
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292 protein IDs. |
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293 |
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294 ## [v0.5.5] - 2021-02-28 |
19 | 295 [v0.5.5]: https://github.com/zellerlab/GECCO/compare/v0.5.4...v0.5.5 |
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296 ### Fixed |
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297 - `gecco cv` bug causing only the last fold to be written. |
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298 |
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299 ## [v0.5.4] - 2021-02-28 |
19 | 300 [v0.5.4]: https://github.com/zellerlab/GECCO/compare/v0.5.3...v0.5.4 |
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301 ### Changed |
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302 - Replaced `verboselogs`, `coloredlogs` and `better-exceptions` with `rich`. |
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303 ### Removed |
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304 - `tqdm` training dependency. |
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305 ### Added |
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306 - `gecco annotate` command to produce a feature table from a genomic file. |
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307 - `gecco embed` to embed BGCs into non-BGC regions using feature tables. |
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308 |
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309 ## [v0.5.3] - 2021-02-21 |
19 | 310 [v0.5.3]: https://github.com/zellerlab/GECCO/compare/v0.5.2...v0.5.3 |
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311 ### Fixed |
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312 - Coordinates of genes in output GenBank files. |
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313 - Potential issue with the number of CPUs in `PyHMMER.run`. |
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314 ### Changed |
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315 - Bump required `pyrodigal` version to `v0.4.2` to fix buffer overflow. |
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316 |
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317 ## [v0.5.2] - 2021-01-29 |
19 | 318 [v0.5.2]: https://github.com/zellerlab/GECCO/compare/v0.5.1...v0.5.2 |
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319 ### Added |
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320 - Support for downloading HMM files directly from GitHub releases assets. |
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321 - Validation of filtered HMMs with MD5 checksum. |
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322 ### Fixed |
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323 - Invalid coordinates of protein domains in GenBank output files. |
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324 - `gecco.interpro` module not being added to wheel distribution. |
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325 ### Changed |
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326 - Bump required `pyhmmer` version to `v0.2.1`. |
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327 |
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328 ## [v0.5.1] - 2021-01-15 |
19 | 329 [v0.5.1]: https://github.com/zellerlab/GECCO/compare/v0.5.0...v0.5.1 |
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330 ### Fixed |
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331 - `--hmm` flag being ignored in in `gecco run` command. |
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332 - `PyHMMER` using HMM names instead of accessions, causing issues with Pfam HMMs. |
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333 |
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334 ## [v0.5.0] - 2021-01-11 |
19 | 335 [v0.5.0]: https://github.com/zellerlab/GECCO/compare/v0.4.5...v0.5.0 |
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336 ### Added |
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337 - Explicit support for Python 3.9. |
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338 ### Changed |
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339 - [`pyhmmer`](https://pypi.org/project/pyhmmer) is used to annotate protein sequences instead of HMMER3 binary `hmmsearch`. |
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340 - HMM files are stored in binary format to speedup parsing and reduce storage size. |
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341 - `tqdm` is now a *training*-only dependency. |
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342 - `gecco cv` now requires *training* dependencies. |
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343 |
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344 ## [v0.4.5] - 2020-11-23 |
19 | 345 [v0.4.5]: https://github.com/zellerlab/GECCO/compare/v0.4.4...v0.4.5 |
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346 ### Added |
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347 - Additional `fold` column to cross-validation table output. |
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348 ### Changed |
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349 - Use sequence ID instead of protein ID to extract type from cluster in `gecco cv`. |
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350 - Install HMM data in pre-pressed format to make `hmmsearch` runs faster on short sequences. |
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351 - `gecco.orf` was rewritten to extract genes from input sequences in parallel. |
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352 |
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353 ## [v0.4.4] - 2020-09-30 |
19 | 354 [v0.4.4]: https://github.com/zellerlab/GECCO/compare/v0.4.3...v0.4.4 |
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355 ### Added |
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356 - `gecco cv loto` command to run LOTO cross-validation using BGC types |
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357 for stratification. |
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358 - `header` keyword argument to `FeatureTable.dump` and `ClusterTable.dump` |
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359 to write the table without the column header allowing to append to an |
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360 existing table. |
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361 - `__getitem__` implementation for `FeatureTable` and `ClusterTable` |
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362 that returns a single row or a sub-table from a table. |
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363 ### Fixed |
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364 - `gecco cv` command now writes results iteratively instead of holding |
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365 the tables for every fold in memory. |
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366 ### Changed |
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367 - Bumped `pandas` training dependency to `v1.0`. |
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368 |
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369 ## [v0.4.3] - 2020-09-07 |
19 | 370 [v0.4.3]: https://github.com/zellerlab/GECCO/compare/v0.4.2...v0.4.3 |
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371 ### Fixed |
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372 - GenBank files being written with invalid `/cds` feature type. |
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373 ### Changed |
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374 - Blocked installation of Biopython `v1.78` or newer as it removes `Bio.Alphabet` |
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375 and breaks the current code. |
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376 |
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377 ## [v0.4.2] - 2020-08-07 |
19 | 378 [v0.4.2]: https://github.com/zellerlab/GECCO/compare/v0.4.1...v0.4.2 |
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379 ### Fixed |
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380 - `TypeClassifier.predict_types` using inverse type probabilities when |
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381 given several clusters to process. |
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382 |
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383 ## [v0.4.1] - 2020-08-07 |
19 | 384 [v0.4.1]: https://github.com/zellerlab/GECCO/compare/v0.4.0...v0.4.1 |
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385 ### Fixed |
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386 - `gecco run` command crashing on input sequences not containing any genes. |
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387 |
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388 ## [v0.4.0] - 2020-08-06 |
19 | 389 [v0.4.0]: https://github.com/zellerlab/GECCO/compare/v0.3.0...v0.4.0 |
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390 ### Added |
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391 - `gecco.model.ProductType` enum to model the biosynthetic class of a BGC. |
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392 ### Removed |
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393 - `pandas` interaction from internal data model. |
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394 - `ClusterCRF` code specific to cross-validation. |
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395 ### Changed |
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396 - `pandas`, `fisher` and `statsmodels` dependencies are now optional. |
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397 - `gecco train` command expects a cluster table in addition to the feature |
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398 table to know the types of the input BGCs. |
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399 |
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400 ## [v0.3.0] - 2020-08-03 |
19 | 401 [v0.3.0]: https://github.com/zellerlab/GECCO/compare/v0.2.2...v0.3.0 |
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402 ### Changed |
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403 - Replaced Nearest-Neighbours classifier with Random Forest to perform type |
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404 prediction for candidate BGCs. |
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405 - `gecco.knn` module was renamed to implementation-agnostic name `gecco.types`. |
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406 ### Fixed |
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407 - Extraction of domain composition taking a long time in `gecco train` command. |
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408 ### Removed |
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409 - `--metric` argument to the `gecco run` CLI command. |
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410 |
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411 ## [v0.2.2] - 2020-07-31 |
19 | 412 [v0.2.2]: https://github.com/zellerlab/GECCO/compare/v0.2.1...v0.2.2 |
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413 ### Changed |
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414 - `Domain` and `Gene` can now carry qualifiers that are used when they |
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415 are translated to a sequence feature. |
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416 ### Added |
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417 - InterPro names, accessions, and HMMER e-value for each annotated domain |
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418 in GenBank output files. |
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419 |
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420 ## [v0.2.1] - 2020-07-23 |
19 | 421 [v0.2.1]: https://github.com/zellerlab/GECCO/compare/v0.2.0...v0.2.1 |
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422 ### Fixed |
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423 - Various potential crashes in `ClusterRefiner` code. |
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424 ### Removed |
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425 - Uneeded feature dictionary filtering in `ClusterCRF` for models with |
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426 Fisher Exact Test feature selection. |
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427 |
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428 ## [v0.2.0] - 2020-07-23 |
19 | 429 [v0.2.0]: https://github.com/zellerlab/GECCO/compare/v0.1.1...v0.2.0 |
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430 ### Fixed |
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431 - `pandas` warning about unsorted columns in `gecco run`. |
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432 ### Removed |
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433 - `Gene.probability` property, replaced by `Gene.maximum_probability` and |
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434 `Gene.average_probability` properties to be explicit. |
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435 ### Changed |
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436 - Internal model now uses `Pfam` and `Tigrfam` with the top 35% features |
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437 selected with Fisher's Exact Test. |
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438 - `ClusterRefiner` now removes genes on `Cluster` edges if they do not |
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439 contain any domain annotation. |
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440 |
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441 ## [v0.1.1] - 2020-07-22 |
19 | 442 [v0.1.1]: https://github.com/zellerlab/GECCO/compare/v0.1.0...v0.1.1 |
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443 ### Added |
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444 - `ClusterCRF.predict_probabilities` to annotate a list of `Gene`. |
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445 ### Changed |
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446 - BGC probability is now stored at the `Domain` level instead of at the `Gene` |
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447 level, independently of the feature extraction level used by the CRF. |
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448 - `ClusterKNN` will use the model path provided to `gecco run` if any. |
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449 ### Docs |
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450 - Added this changelog file to document changes in the code. |
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451 - Added documentation to `gecco` submodules missing some. |
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452 - Included the `CHANGELOG.md` file to the generated docs. |
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453 |
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454 ## [v0.1.0] - 2020-07-17 |
19 | 455 [v0.1.0]: https://github.com/zellerlab/GECCO/compare/v0.0.1...v0.1.0 |
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456 Initial release. |
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457 |
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458 ## [v0.0.1] - 2018-08-13 |
19 | 459 [v0.0.1]: https://github.com/zellerlab/GECCO/compare/37afb97...v0.0.1 |
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460 Proof-of-concept. |