v0.9.0

A release with a HUGE breaking change.

Until now, we have been using the word "predicate" in two contexts:

• VariantPredicate for testing if a variant meets one or more criteria (is missense, is a SNV, ...)
• genotype/phenotype predicate for assigning an individual into a genotype/phenotype category

The first context stays as is. However, from now on, we will use "classifier" and "class" for the assignment of an individual into a genotype/phenotype category.

Sadly, this results in a huge breaking change and practically all analyses will have to be updated. We outline the migration strategy below.

Migration strategy

A list of the most important updates

Item	Replacement	Comment
gpsea.analysis.predicate.genotype.VariantPredicate	gpsea.analysis.predicate.VariantPredicate	Moved with no change
gpsea.analysis.predicate.genotype.VariantPredicates	gpsea.analysis.predicate	The builtin predicates are now available in the module
gpsea.analysis.predicate.genotype.GenotypePolyPredicate	gpsea.analysis.clf.GenotypeClassifier	Moved and renamed
gpsea.analysis.predicate.phenotype.PhenotypePolyPredicate	gpsea.analysis.clf.PhenotypeClassifier	Moved and renamed
gpsea.analysis.predicate.genotype.monoallelic_predicate	gpsea.analysis.clf.monoallelic_classifier	Moved and renamed
gpsea.analysis.predicate.genotype.biallelic_predicate	gpsea.analysis.clf.biallelic_classifier	Moved and renamed
gpsea.analysis.predicate.genotype.allele_count	gpsea.analysis.clf.allele_count	Moved and renamed
gpsea.analysis.predicate.genotype.sex_predicate	gpsea.analysis.clf.sex_classifier	Moved and renamed
gpsea.analysis.predicate.genotype.diagnosis_predicate	gpsea.analysis.clf.diagnosis_classifier	Moved and renamed
gpsea.analysis.predicate.phenotype.prepare_predicates_for_terms_of_interest	gpsea.analysis.clf.prepare_classifiers_for_terms_of_interest	Moved and renamed

Please contact ielis to help with analysis migration.

What's Changed

• Use classifiers instead of genotype/phenotype predicates. by @ielis in #381

Full Changelog: v0.8.0...v0.9.0

v0.8.0

What's Changed

• Revise reports by @ielis in #354
• Include test statistics (not just the p values) by @pnrobinson in #357
• Harmonize caching by @ielis in #361
• Update documentation for CountingPhenotypeScorer by @pnrobinson in #360
• Add TRANSMEMBRANE and TOPOLOGICAL DOMAIN to protein types by @pnrobinson in #359
• Fetch a few more feature types from Uniprot by @ielis in #369
• CohortViewer needs transcript ID to visualize a cohort by @ielis in #370
• Report analysis errors by @ielis in #372
• Use Ruff to lint and format by @ielis in #374
• Remove case study notebooks by @ielis in #375
• Remove dev files by @ielis in #376
• Enhance the documentation, explain genotype predicates with figures by @ielis in #348
• Improve the docs for specified terms MT filter by @ielis in #378
• Ignore the inconsistent transcripts when getting transcripts for a gene from Variant Validator by @ielis in #379

Full Changelog: v0.7.1...v0.8.0

v0.7.1

What's Changed

• Add convenience methods on Cohort and result items by @ielis in #347
• Parse onsets formatted as ontology terms by @ielis in #350
• Simplify the HPO term analysis configuration by @ielis in #351
• adding zinc finger to ProteinFeature by @pnrobinson in #346
• DeVries score update by @pnrobinson in #352

Full Changelog: v0.7.0...v0.7.1

v0.7.0

What's Changed

• Use ancestors to implement HPO phenotype predicate by @ielis in #325
• Simplify the mode of inheritance predicates by @ielis in #307
• Simplify the variant predicates that target protein features by @ielis in #329
• Improve docs for the VariantPredicates.region predicate by @ielis in #330
• Generalize analysis results by @ielis in #331
• Show how to plot Kaplan-Meier curves by @ielis in #332
• Standardize metadata of the analysis components by @ielis in #334
• Counting male and female individuals for CohortViewer by @pnrobinson in #328
• Expose more analysis components by @ielis in #336
• Fix Q/C reporting by @ielis in #337

Full Changelog: v0.6.0...v0.7.0

v0.6.0

What's Changed

• Added exons to variant viewer by @lnrekerle in #300
• Sanitize SpecifyTermsMtcFilter input by @ielis in #309
• Minor issue and bug fixes by @ielis in #319
• Add survival analyses by @ielis in #320
• Sort variant effects table and report percentages by @pnrobinson in #310
• Ask for the predicate group labels individually by @ielis in #322
• Refactor gpsea.view package elements by @ielis in #323

Full Changelog: v0.5.0...v0.6.0

v0.5.0

What's Changed

• Simplify the autosomal recessive and biallelic predicates by @ielis in #293
• Allow using measurements as phenotype scores by @ielis in #289
• Improve protein variant table by @pnrobinson in #292
• Fix bug if there are no protein features by @lnrekerle in #297
• Update tests to reflect the genotype category label changes by @ielis in #302
• Allow to filter on annotation frequency by @pnrobinson in #299
• Remove HMF04 from HPO MTC filter by @ielis in #288
• The nan phenotype scores will be ignored by @ielis in #303
• Remove notebooks by @pnrobinson in #298

Full Changelog: v0.4.1...v0.5.0

v0.4.1

What's Changed

• Ensure the logical predicates are hashable by @ielis in #271
• Minor Uniprot service updates by @ielis in #274
• DataFrame for protein features by @pnrobinson in #273
• Adding imprecise SVs by @pnrobinson in #260
• Relax handling of the MTC filtering by @ielis in #280
• Uniprot JSON prototype by @pnrobinson in #277
• Document protein domain visualization by @pnrobinson in #279

Full Changelog: v0.4.0...v0.4.1

v0.4.0

What's Changed

• Remove gpsea.data module by @ielis in #247
• Update documentation by @pnrobinson in #251
• Improve summarize by @ielis in #254
• Add codes to MTC filter summary, improve HPO term reporting by @ielis in #257
• Counts table by @pnrobinson in #255
• Test phenotype predicate utility methods by @ielis in #256
• A minor doc fix by @ielis in #258
• Improve mode of inheritance handling by @ielis in #264
• Simplify MoI predicates by @ielis in #265
• Fix Uniprot API bug by @ielis in #266
• Improve Pydoc for allelic predicates by @ielis in #267
• updated tqdm to print files/sec instead of it/sec by @lnrekerle in #248

Full Changelog: v0.3.0...v0.4.0

v0.3.0

What's Changed

• Improve the MTC user guide section by @ielis in #234
• Updates all the notebooks to use gpsea by @lnrekerle in #235
• Create de Vries scorer, support wrapping phenotype scoring function by @ielis in #232
• Handle inheritance modes by @ielis in #239
• Prevent creating a cohort from individuals who include duplicates by @lnrekerle in #238
• Simplify phenopacket loading functions by @ielis in #242
• Add T test by @ielis in #243
• Remove obsolete analysis code by @ielis in #244
• Allow using Sex and disease diagnosis as a genotype predicate by @ielis in #245

Full Changelog: v0.2.0...v0.3.0

v0.2.0

A lot of progress was made since the last version.

What's Changed

• Prepare logic for fetching transcript regions for visualization by @ielis in #67
• Fixed bugs that came up with a subjects in RPGRIP by @lnrekerle in #68
• Finish extending transcript exon model by @ielis in #70
• Set is_preferred annotation by @ielis in #74
• Moved VariantEffects so it's using the Enum by @lnrekerle in #78
• HGVSVariantCoordinatesFinder by @frehburg in #77
• Created Cohort Viewer that shows excluded patients by @lnrekerle in #85
• Fix change length bug by @ielis in #94
• Streamline predicate/analysis workflow by @ielis in #88
• Created new file testing groups against each other by @lnrekerle in #99
• Add methods for simple genome arithmetics by @ielis in #101
• Used tqdm to create a progress bar by @lnrekerle in #107
• Improve error messages by @lnrekerle in #96
• Update notebooks by @lnrekerle in #121
• Removing redundant phenopacket generation code by @pnrobinson in #116
• Add files for PPP2R1A by @pnrobinson in #80
• Removing redundant phenopacket gen code SUOX by @pnrobinson in #115
• removing redudant code to gen phenopackets and adding phenopackets fr… by @pnrobinson in #117
• Setup notebook for visualizers by @ielis in #114
• Run notebooks in CI by @ielis in #122
• Formalize handling and reporting of input errors by @ielis in #128
• Fix bug in summarizing errors and warnings of the notepad. by @ielis in #129
• Add visualization prose by @ielis in #125
• Improve protein service by @lnrekerle in #130
• Humanize the analysis runner by @ielis in #131
• Contextualize the count with the cohort size in the G/P result summary by @ielis in #132
• Changed all occurrences of hgvsc_id to hgvs_cdna by @lnrekerle in #138
• Isolate G/P code by @ielis in #136
• Add Disease to Patient by @lnrekerle in #143
• CLDN16 by @pnrobinson in #146
• Draw variants transcript and protein by @pnrobinson in #148
• Fixed the count issue with summarize by @lnrekerle in #145
• Kbg by @pnrobinson in #154
• Added testing for disease predicates by @lnrekerle in #151
• Update the GitHub action names by @ielis in #158
• Use SUOX cohort as a real-life test data, add JSON (de)serialization by @ielis in #157
• Buffer vv response by @pnrobinson in #155
• Mtc by @pnrobinson in #160
• protein drawing by @pnrobinson in #162
• KMT2D by @pnrobinson in #166
• Restore the deleted test_data_dir fixture by @ielis in #168
• Added disease viewable, variant and effect counts by @lnrekerle in #167
• Check protein coordinates by @ielis in #170
• Kmt2 d by @pnrobinson in #169
• Notebooks all work. Small changes so tables look good. by @lnrekerle in #173
• Created ProteinRegionPredicate by @lnrekerle in #175
• Adding new MTC filter that allows the user to specific which term(s) … by @pnrobinson in #177
• More mtc heuristic by @pnrobinson in #178
• fixing template to have blocks appear underneath each other by @pnrobinson in #182
• Create Protein table so users can see list of protein features and coordinates by @lnrekerle in #179
• Merge Protein Visualizer into develop by @frehburg in #184
• Implement variant predicates and allele counter by @ielis in #159
• Created a Formatter by @lnrekerle in #185
• Fix bug in validation of terms to test in "specify terms" MTC strategy by @ielis in #195
• Removed the red background by @lnrekerle in #193
• multiple testing documentation by @pnrobinson in #189
• Add support for large imprecise SVs by @ielis in #196
• Add section about statistical tests into the documentation by @pnrobinson in #198
• Implement IsStructuralVariantPredicate for testing if a variant is an SV by @ielis in #199
• Add CountingPhenotypePredicate by @ielis in #197
• Updating MTC heuristic and documentation by @pnrobinson in #200
• Expanded table of genotypes by @lnrekerle in #205
• Fix some bugs by @ielis in #208
• Implement logical inversion of a variant predicate by @ielis in #206
• Exemplify usage of the counting predicate on RERE cohort by @ielis in #202
• Reporting the number of tests in GenotypePhenotypeAnalysisResult by @lnrekerle in #209
• Fixing "Division by 0" error by @lnrekerle in #214
• Fixed large variants in variant_key and added documentation and a test. by @lnrekerle in #204
• Demonstrate testing correlation between genotype groups and phenotype score by @ielis in #219
• Fix bug in change length calculation for CNVs by @ielis in #220
• Improve phenotype and MTC filtering by @ielis in #221
• Remove name from Phenotype. by @ielis in #224
• updating tutorial documentation by @pnrobinson in #226
• Update tutorial by @ielis in #225
• Do not run notebooks in CI by @ielis in #229
• Change the project name to GPSEA by @ielis in #230
• Split analysis package into analysis types by @ielis in #231

New Contributors

• @frehburg made their first contribution in #77

Full Changelog: v0.1.0...v0.2.0