annotate CHANGELOG.md @ 13:fde43648cba0 draft

"Release v0.9.1-alpha4"
author althonos
date Thu, 31 Mar 2022 18:00:15 +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]
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8 [Unreleased]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha4...master
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9
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10 ## [v0.9.1-alpha4] - 2022-03-31
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11 [v0.9.1-alpha4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha3...v0.9.1-alpha4
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12
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13 Retrain internal model with:
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14 ```
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15 $ python -m gecco -vv train --c1 0.4 --c2 0 --select 0.25 --window-size 20 \
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16 -f mibig-2.0.proG2.Pfam-v35.0.features.tsv \
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17 -c mibig-2.0.proG2.clusters.tsv \
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18 -g GECCO-data/data/embeddings/mibig-2.0.proG2.genes.gff \
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19 -o models/v0.9.1-alpha4
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20 ```
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21
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22 ## [v0.9.1-alpha3] - 2022-03-23
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23 [v0.9.1-alpha3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha2...v0.9.1-alpha3
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24
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25 ### Added
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26 - `gecco.model.GeneTable` class to store gene coordinates independently of protein domains.
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27
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28 ### Changed
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29 - Refactored implementation of `load` and `dump` methods for `Table` classes into a dedicated base class.
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30 - `gecco run` and `gecco annotate` now output a gene table in addition to the feature and cluster tables.
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31 - `gecco train` expects a gene table instead of a GFF file for the gene coordinates.
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33 ## [v0.9.1-alpha2] - 2022-03-23
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34 [v0.9.1-alpha2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha1...v0.9.1-alpha2
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35
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36 ### Fixed
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37 - `TypeClassifier.trained` not being able to read unknown types from type tables.
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38
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39 ## [v0.9.1-alpha1] - 2022-03-20
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40 [v0.9.1-alpha1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.10...v0.9.1-alpha1
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41 Candidate release with support for a sliding window in the CRF prediction algorithm.
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42
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43 ## [v0.8.10] - 2022-02-23
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44 [v0.8.10]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.9...v0.8.10
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45 ### Fixed
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46 - `--antismash-sideload` flag of `gecco run` causing command to crash.
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47
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48 ## [v0.8.9] - 2022-02-22
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49 [v0.8.9]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.8...v0.8.9
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50 ### Removed
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51 - Prediction and support for the *Other* biosynthetic type of MIBiG clusters.
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52
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53 ## [v0.8.8] - 2022-02-21
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54 [v0.8.8]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.7...v0.8.8
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55 ### Fixed
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56 - `ClusterRefiner` filtering method for edge genes not working as intended.
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57 - `gecco run` and `gecco annotate` commands crashing on missing input files instead of nicely rendering the error.
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58
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59 ## [v0.8.7] - 2022-02-18
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60 [v0.8.7]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.6...v0.8.7
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61 ### Fixed
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62 - `interpro.json` metadata file not being included in distribution files.
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63 - Missing docstring for `Protein.with_domains` method.
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64 ### Changed
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65 - Bump minimum `scikit-learn` version to `v1.0` for Python3.7+.
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66
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67 ## [v0.8.6] - 2022-02-17 - YANKED
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68 [v0.8.6]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.5...v0.8.6
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69 ### Added
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70 - CLI flag for enabling region masking for contigs processed by Prodigal.
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71 - CLI flag for controlling region distance used for edge distance filtering.
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72 ### Changed
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73 - `gecco.model.Gene` and `gecco.model.Protein` are now immutable data classes.
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74 - Bump minimum `pyrodigal` version to `v0.6.4` to use region masking.
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75 - Implement filtering for extracted clusters based on distance to the contig edge.
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76 - Store InterPro metadata file uncompressed for version-control integration.
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77 ### Fixed
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78 - Mark `BGC0000930` as `Terpene` in the type classifier data.
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79 - Progress bar messages are now in consistent format.
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81 ## [v0.8.5] - 2021-11-21
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82 [v0.8.5]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.4...v0.8.5
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83 ### Added
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84 - Minimal compatibility support for running GECCO inside of Galaxy workflows.
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85
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86 ## [v0.8.4] - 2021-09-26
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87 [v0.8.4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.3-post1...v0.8.4
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88 ### Fixed
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89 - `gecco convert gbk --format bigslice` failing to run because of outdated code ([#5](https://github.com/zellerlab/GECCO/issues/5)).
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90 - `gecco convert gbk --format bigslice` not creating files with names conforming to BiG-SLiCE expected input.
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91 ### Changed
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92 - Bump minimum `pyrodigal` version to `v0.6.2` to use platform-accelerated code if supported.
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93
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94 ## [v0.8.3-post1] - 2021-08-23
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95 [v0.8.3-post1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.3...v0.8.3-post1
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96 ### Fixed
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97 - Wrong default value for `--threshold` being shown in `gecco run` help message.
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98
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99 ## [v0.8.3] - 2021-08-23
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100 [v0.8.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.2...v0.8.3
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101 ### Changed
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102 - Default probability threshold for segmentation to 0.3 (from 0.4).
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103
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104 ## [v0.8.2] - 2021-07-31
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105 [v0.8.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.1...v0.8.2
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106 ### Fixed
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107 - `gecco run` crashing on Python 3.6 because of missing `contextlib.nullcontext` class.
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108 ### Changed
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109 - `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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110 - `PyHMMER.run` now reports the *p-value* of each domain in addition to the *e-value* as a `/note` qualifier.
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111
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112 ## [v0.8.1] - 2021-07-29
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113 [v0.8.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.0...v0.8.1
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114 ### Changed
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115 - `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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116 ### Fixed
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117 - `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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118 ### Added
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119 - Missing documentation for the `strand` attribute of `gecco.model.Gene`.
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120
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121 ## [v0.8.0] - 2021-07-03
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122 [v0.8.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.7.0...v0.8.0
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123 ### Changed
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124 - Retrain internal model using new sequence embeddings and remove broken/duplicate BGCs from MIBiG 2.0.
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125 - Bump minimum `pyhmmer` version to `v0.4.0` to improve exception handling.
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126 - Bump minimum `pyrodigal` version to `v0.5.0` to fix sequence decoding on some platforms.
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127 - Use p-values instead of e-values to filter domains obtained with HMMER.
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128 - `gecco cv` and `gecco train` now seed the RNG with a user-defined seed before shuffling rows of training data.
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129 ### Fixed
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130 - Extraction of BGC compositions for the type predictor while training.
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131 - `ClusterCRF.trained` failing to open an external model.
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132 ### Added
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133 - `Domain.pvalue` attribute to access the p-value of a domain annotation.
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134 - Mandatory `pvalue` column to `FeatureTable` objects.
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135 - Support for loading several feature tables in `gecco train` and `gecco cv`.
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136 - Warnings to `ClusterCRF.fit` when selecting uninformative features.
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137 - `--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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138 ### Removed
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139 - Outdated `gecco embed` command.
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140 - Unused `--truncate` flag from the `gecco train` CLI.
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141 - Tigrfam domains, which is not improving performance on the new training data.
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142
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143 ## [v0.7.0] - 2021-05-31
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144 [v0.7.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.3...v0.7.0
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145 ### Added
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146 - Support for writing an AntiSMASH sideload JSON file after a `gecco run` workflow.
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147 - Code for converting GenBank files in BiG-SLiCE compatible format with the `gecco convert` subcommand.
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148 - Documentation about using GECCO in combination with AntiSMASH or BiG-SLiCE.
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149 ### Changed
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150 - Minimum Biopython version to `v1.73` for compatibility with older bioinformatics tooling.
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151 - Internal domain composition shipped in the `gecco.types` with newer composition array obtained directly from MIBiG files.
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152 ### Removed
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153 - Outdated notice about `-vvv` verbosity level in the help message of the main `gecco` command.
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154
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155 ## [v0.6.3] - 2021-05-10
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156 [v0.6.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.2...v0.6.3
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157 ### Fixed
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158 - HMMER annotation not properly handling inputs with multiple contigs.
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159 - Some progress bar totals displaying as floats in the CLI.
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160 ### Changed
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161 - `PyHMMER` now sets the `Z` and `domZ` values from the number of proteins given to the search pipeline.
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162 - `gecco.cli` delegates imports to make CLI more responsive.
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163 - `pkg_resources` has been replaced with `importlib.resources` and `importlib.metadata` where applicable.
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164 - `multiprocessing.cpu_count` has been replaced with `os.cpu_count` where applicable.
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165
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166 ## [v0.6.2] - 2021-05-04
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167 [v0.6.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.1...v0.6.2
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168 ### Fixed
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169 - `gecco cv loto` crashing because of outdated code.
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170 ### Changed
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171 - Logging-style prompt will only display if GECCO is running with `-vv` flag.
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172 ### Added
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173 - GECCO bioRxiv paper reference to `Cluster.to_seq_record` output record.
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174
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175 ## [v0.6.1] - 2021-03-15
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176 [v0.6.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.0...v0.6.1
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177 ### Fixed
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178 - Progress bar not being disabled by `-q` flag in CLI.
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179 - Fallback to using HMM name if accession is not available in `PyHMMER`.
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180 - Group genes by source contig and process them separately in `PyHMMER` to avoid bogus E-values.
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181 ### Added
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182 - `psutil` dependency to get the number of physical CPU cores on the host machine.
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183 - Support for using an arbitrary mapping of positives to negatives in `gecco embed`.
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184 ### Removed
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185 - Unused and outdated `HMMER` and `DomainRow` classes from `gecco.hmmer`.
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186
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187 ## [v0.6.0] - 2021-02-28
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188 [v0.6.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.5...v0.6.0
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189 ### Changed
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190 - Updated internal model with a cleaned-up version of the MIBiG-2.0
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althonos
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191 Pfam-33.1/Tigrfam-15.0 embedding.
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192 - Updated internal InterPro catalog.
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193 ### Fixed
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194 - Features not being grouped together in `gecco cv` and `gecco train`
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195 when provided with a feature table where rows were not sorted by
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196 protein IDs.
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197
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198 ## [v0.5.5] - 2021-02-28
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199 [v0.5.5]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.4...v0.5.5
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200 ### Fixed
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althonos
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201 - `gecco cv` bug causing only the last fold to be written.
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202
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203 ## [v0.5.4] - 2021-02-28
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204 [v0.5.4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.3...v0.5.4
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205 ### Changed
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206 - Replaced `verboselogs`, `coloredlogs` and `better-exceptions` with `rich`.
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207 ### Removed
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208 - `tqdm` training dependency.
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althonos
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209 ### Added
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210 - `gecco annotate` command to produce a feature table from a genomic file.
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althonos
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211 - `gecco embed` to embed BGCs into non-BGC regions using feature tables.
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212
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213 ## [v0.5.3] - 2021-02-21
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214 [v0.5.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.2...v0.5.3
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215 ### Fixed
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216 - Coordinates of genes in output GenBank files.
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217 - Potential issue with the number of CPUs in `PyHMMER.run`.
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218 ### Changed
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219 - Bump required `pyrodigal` version to `v0.4.2` to fix buffer overflow.
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220
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221 ## [v0.5.2] - 2021-01-29
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222 [v0.5.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.1...v0.5.2
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223 ### Added
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224 - Support for downloading HMM files directly from GitHub releases assets.
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225 - Validation of filtered HMMs with MD5 checksum.
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226 ### Fixed
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227 - Invalid coordinates of protein domains in GenBank output files.
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althonos
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228 - `gecco.interpro` module not being added to wheel distribution.
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229 ### Changed
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230 - Bump required `pyhmmer` version to `v0.2.1`.
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231
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232 ## [v0.5.1] - 2021-01-15
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233 [v0.5.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.0...v0.5.1
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234 ### Fixed
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235 - `--hmm` flag being ignored in in `gecco run` command.
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236 - `PyHMMER` using HMM names instead of accessions, causing issues with Pfam HMMs.
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237
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althonos
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238 ## [v0.5.0] - 2021-01-11
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239 [v0.5.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.5...v0.5.0
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240 ### Added
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althonos
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241 - Explicit support for Python 3.9.
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242 ### Changed
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243 - [`pyhmmer`](https://pypi.org/project/pyhmmer) is used to annotate protein sequences instead of HMMER3 binary `hmmsearch`.
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244 - HMM files are stored in binary format to speedup parsing and reduce storage size.
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245 - `tqdm` is now a *training*-only dependency.
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althonos
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246 - `gecco cv` now requires *training* dependencies.
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247
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248 ## [v0.4.5] - 2020-11-23
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249 [v0.4.5]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.4...v0.4.5
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250 ### Added
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251 - Additional `fold` column to cross-validation table output.
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althonos
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252 ### Changed
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253 - Use sequence ID instead of protein ID to extract type from cluster in `gecco cv`.
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althonos
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254 - Install HMM data in pre-pressed format to make `hmmsearch` runs faster on short sequences.
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althonos
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255 - `gecco.orf` was rewritten to extract genes from input sequences in parallel.
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256
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257 ## [v0.4.4] - 2020-09-30
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258 [v0.4.4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.3...v0.4.4
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259 ### Added
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260 - `gecco cv loto` command to run LOTO cross-validation using BGC types
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althonos
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261 for stratification.
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althonos
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262 - `header` keyword argument to `FeatureTable.dump` and `ClusterTable.dump`
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althonos
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263 to write the table without the column header allowing to append to an
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264 existing table.
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althonos
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265 - `__getitem__` implementation for `FeatureTable` and `ClusterTable`
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266 that returns a single row or a sub-table from a table.
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267 ### Fixed
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althonos
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268 - `gecco cv` command now writes results iteratively instead of holding
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althonos
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269 the tables for every fold in memory.
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althonos
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270 ### Changed
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271 - Bumped `pandas` training dependency to `v1.0`.
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272
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273 ## [v0.4.3] - 2020-09-07
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274 [v0.4.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.2...v0.4.3
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275 ### Fixed
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althonos
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276 - GenBank files being written with invalid `/cds` feature type.
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277 ### Changed
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278 - Blocked installation of Biopython `v1.78` or newer as it removes `Bio.Alphabet`
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279 and breaks the current code.
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280
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281 ## [v0.4.2] - 2020-08-07
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282 [v0.4.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.1...v0.4.2
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283 ### Fixed
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althonos
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284 - `TypeClassifier.predict_types` using inverse type probabilities when
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althonos
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285 given several clusters to process.
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286
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althonos
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287 ## [v0.4.1] - 2020-08-07
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288 [v0.4.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.0...v0.4.1
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289 ### Fixed
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althonos
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290 - `gecco run` command crashing on input sequences not containing any genes.
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291
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292 ## [v0.4.0] - 2020-08-06
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293 [v0.4.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.3.0...v0.4.0
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294 ### Added
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295 - `gecco.model.ProductType` enum to model the biosynthetic class of a BGC.
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296 ### Removed
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297 - `pandas` interaction from internal data model.
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298 - `ClusterCRF` code specific to cross-validation.
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299 ### Changed
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300 - `pandas`, `fisher` and `statsmodels` dependencies are now optional.
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301 - `gecco train` command expects a cluster table in addition to the feature
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302 table to know the types of the input BGCs.
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303
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304 ## [v0.3.0] - 2020-08-03
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305 [v0.3.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.2.2...v0.3.0
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306 ### Changed
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307 - Replaced Nearest-Neighbours classifier with Random Forest to perform type
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308 prediction for candidate BGCs.
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309 - `gecco.knn` module was renamed to implementation-agnostic name `gecco.types`.
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310 ### Fixed
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311 - Extraction of domain composition taking a long time in `gecco train` command.
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312 ### Removed
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313 - `--metric` argument to the `gecco run` CLI command.
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314
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315 ## [v0.2.2] - 2020-07-31
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316 [v0.2.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.2.1...v0.2.2
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317 ### Changed
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318 - `Domain` and `Gene` can now carry qualifiers that are used when they
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319 are translated to a sequence feature.
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320 ### Added
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321 - InterPro names, accessions, and HMMER e-value for each annotated domain
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322 in GenBank output files.
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323
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324 ## [v0.2.1] - 2020-07-23
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325 [v0.2.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.2.0...v0.2.1
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326 ### Fixed
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327 - Various potential crashes in `ClusterRefiner` code.
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328 ### Removed
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329 - Uneeded feature dictionary filtering in `ClusterCRF` for models with
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330 Fisher Exact Test feature selection.
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331
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332 ## [v0.2.0] - 2020-07-23
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333 [v0.2.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.1.1...v0.2.0
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334 ### Fixed
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335 - `pandas` warning about unsorted columns in `gecco run`.
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336 ### Removed
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337 - `Gene.probability` property, replaced by `Gene.maximum_probability` and
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338 `Gene.average_probability` properties to be explicit.
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339 ### Changed
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340 - Internal model now uses `Pfam` and `Tigrfam` with the top 35% features
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341 selected with Fisher's Exact Test.
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342 - `ClusterRefiner` now removes genes on `Cluster` edges if they do not
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343 contain any domain annotation.
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344
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345 ## [v0.1.1] - 2020-07-22
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346 [v0.1.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.1.0...v0.1.1
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347 ### Added
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348 - `ClusterCRF.predict_probabilities` to annotate a list of `Gene`.
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349 ### Changed
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350 - BGC probability is now stored at the `Domain` level instead of at the `Gene`
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351 level, independently of the feature extraction level used by the CRF.
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352 - `ClusterKNN` will use the model path provided to `gecco run` if any.
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353 ### Docs
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354 - Added this changelog file to document changes in the code.
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355 - Added documentation to `gecco` submodules missing some.
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356 - Included the `CHANGELOG.md` file to the generated docs.
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357
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358 ## [v0.1.0] - 2020-07-17
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359 [v0.1.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.0.1...v0.1.0
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360 Initial release.
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361
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362 ## [v0.0.1] - 2018-08-13
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363 [v0.0.1]: https://git.embl.de/grp-zeller/GECCO/compare/37afb97...v0.0.1
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364 Proof-of-concept.