gentropy 2.0.0

v2.0.0

on Python PyPI

What's Changed

💥 Breaking

• [l2g!] implement new training strategy splitting between EFO/gene pairs and with cross validation (#938) @Irene López Santiago
• [L2GFeatureMatrix!] streamline feature matrix management (#745) @Irene López Santiago
• [Orchestration!] drop airflow orchestration layer from gentropy (#758) @Szymon Szyszkowski

✨ Feature

• adding GERP conservation score to variant annotation (#933) @Daniel Suveges
• allow building package from tag (#930) @Szymon Szyszkowski
• coalesce l2g fm and predictions (#934) @Szymon Szyszkowski
• coalescing the datasets (#932) @Szymon Szyszkowski
• [gold_standard] add traitFromSourceMappedId to schema (#924) @Irene López Santiago
• changing studylocus validation to 95 percent credible sets (#921) @Daniel-Considine
• reverting to using finngen 95% credible sets (#922) @Daniel-Considine
• [variant index] variant description to summarise variant consequences in transcripts (#914) @Daniel Suveges
• redefine neighbourhood features to represent similarity with best metric + other fixes (#913) @Irene López Santiago
• gzip evicence output to match existing format (#915) @Szymon Szyszkowski
• [gold_standard] arbitrary gold standards (#912) @Szymon Szyszkowski
• changes to PICS credible sets (OUT_OF_SAMPLE_LD QC flag and capital PICS) (#910) @Vivien Ho
• extract pos and chromosome from variantid (#909) @Szymon Szyszkowski
• improve partitioning of credible sets (#900) @David Ochoa
• [feature_matrix] extract features for gwas associations only (#901) @Irene López Santiago
• adding l2g features to prediction table (#899) @Daniel Suveges
• [feature_matrix] impute values for gene attribute cols (#895) @Irene López Santiago
• deconvolute studies upon ingestion of GWAS Catalog datasets (#887) @Daniel Suveges
• add effect size direction to coloc output (#854) @Tobi Alegbe
• add step to generate association data (#888) @Vivien Ho
• [trainer] log model explanation with shap (#886) @Irene López Santiago
• flag and filter credible sets (#879) @Tobi Alegbe
• flagging duplicated entries while keeping one of the duplicates (#876) @Daniel Suveges
• making credset qc have an option to coalsce and deduplicate credible sets without ld pruning (#877) @Daniel-Considine
• l2g feature to indicate if gene is protein-coding or not (#873) @xyg123
• [l2g] normalise distance features (#878) @Irene López Santiago
• [l2g_feature_matrix] add credibleSetConfidence to L2G (#875) @Irene López Santiago
• [variant_index] hash variants at the time of instance creation (#874) @Irene López Santiago
• step to export disease/target evidence (#867) @Daniel Suveges
• change betas to posterior mean from susie for Finngen credible sets (#872) @Daniel-Considine
• add gene count features to l2g (#852) @xyg123
• adding desision tree to fine-mapper (#860) @Yakov
• gwas catalog top-hit + study step (#808) @David Ochoa
• [l2g] extend colocalisation neighbourhood metrics to missing genes in the vicinity (#851) @Irene López Santiago
• [susie_finemapper] allow for extraction of the log file from manifest (#859) @Szymon Szyszkowski
• [l2g] limit colocalisation neighbourhood to protein coding genes (#847) @Irene López Santiago
• [coloc] step refactoring (#845) @Szymon Szyszkowski
• adding new LD interface (#759) @Yakov
• enhance variant index partitioning (#834) @David Ochoa
• [l2g] merge sQTL and tuQTL colocalisation features (#824) @Irene López Santiago
• decouple feature generation from L2G training step (#823) @Irene López Santiago
• change LD annotation for PICS fine-mapping to use major ancestry (#821) @Vivien Ho
• optimisation of qc step (#813) @Yakov
• [l2g] implement variant consequence features from VEP (#805) @Irene López Santiago
• fix biosample study validation (#810) @Tobi Alegbe
• add sumstat QC fields to schema (#809) @Yakov
• adding filtering to susie finemapper (#796) @Yakov
• [validation] adding credible set confidence annotation at validation time (#801) @Daniel Suveges
• force reinstallation of the gentropy on the cluster (#804) @Szymon Szyszkowski
• out sample LD qc reason (#798) @David Ochoa
• drop v2g and reimplement distance features (#771) @Irene López Santiago
• change StudyLocusId hashing method to md5 (and change StudyLocusId to string type) (#783) @Vivien Ho
• flag credible sets explained by SuSiE regions (#780) @David Ochoa
• 99% credible set validation during study_locus_validation (#765) @David Ochoa
• add biosample index (#769) @Tobi Alegbe
• adding window based clumping to StudyLocus (#779) @Daniel Suveges
• add studyType to StudyLocus and Colocalisation (and StudyLocusOverlap) (#782) @Vivien Ho
• [dataproc] ability to version gentropy for dataproc cluster (#774) @Szymon Szyszkowski
• flag PICS top hits in studies with credset sumstats (#777) @David Ochoa
• flag all top-hits from GWAS catalog curation (#775) @David Ochoa
• flag MHC credible sets based on lead (#767) @David Ochoa
• [validation] adding credible set variant validation (#757) @Daniel Suveges
• ingest FinnGen UKB meta-analysis data (#756) @Kirill Tsukanov
• adding finemapping method to studylocusid hash (#744) @Daniel-Considine
• [variant index] improved data structure (#710) @Daniel Suveges
• logic and airflow pipeline for validation (#730) @Daniel Suveges
• Finngen r11 ingestion (#733) @Szymon Szyszkowski
• [variant_index] changes for a successful run (#735) @Irene López Santiago
• notebook for locus breaker and susie finemapping benchmark (#717) @Daniel-Considine
• expose summary statistics qc and locus breaker steps to hydra cli (#716) @Szymon Szyszkowski

🐛 Fix

• [l2g_predictions] annotate based on list of features + filter out missing annotation (#925) @Irene López Santiago
• swap the ref parse (#935) @Szymon Szyszkowski
• r2 for lead variant is always 1 (#919) @Yakov
• using the 99% PIP cs column, (#904) @Daniel-Considine
• reclassify eqtl catalogue sc datasets (#894) @Tobi Alegbe
• do not impute isProteinCoding (#902) @Yakov
• ensure the #CHROM is not quoted (#896) @Szymon Szyszkowski
• [credibleSetConfidence] inner join between study locus and variant index to avoid null genes (#890) @Irene López Santiago
• revert distinct for associations input file (#871) @Vivien Ho
• [distance_features] correct mean distance equation and correct rows with negative values (#889) @Irene López Santiago
• fix in calculate_credible_set_log10bf (#868) @Yakov
• logging of finemamper (#870) @Yakov
• add scQTLs into coloc features (#833) @Yakov
• biosample index add efo cell types (#853) @Tobi Alegbe
• adding beta for lead variant (#863) @Yakov
• susie credible sets with unknown confidence (#862) @David Ochoa
• filter nan in CSs (#855) @Yakov
• [eqtl] deduplicating credible set loci (#849) @Daniel Suveges
• updating the susie_finemapper init (#846) @Daniel-Considine
• l2g fixes (#844) @David Ochoa
• fix ukbppp studindex (#839) @Yakov
• [l2g] remove custom session params + other fixes (#841) @Irene López Santiago
• [trainer] drop studyLocusId from training sets (#837) @Irene López Santiago
• [find_overlap] missing right study type in output (#828) @Daniel Suveges
• adding single point statistics to pics loci (#832) @Daniel Suveges
• write mode added to validation steps (#826) @David Ochoa
• empty inSilicoPredictors object in GnomAD variant index (#807) @Daniel Suveges
• mhc flag incorrect (#825) @David Ochoa
• biosample id duplication (#822) @Tobi Alegbe
• adding studId to FM log (#816) @Yakov
• fix of type error in schema checking (#817) @Yakov
• [validation] add qualityControls column if missing in StudyLocus dataset when perfroming validation (#814) @Szymon Szyszkowski
• align the schema of study_index for ukb ppp eur (#803) @Szymon Szyszkowski
• adding data specific p-value filters (#788) @Yakov
• [schema] recursive validation of arbitrarily deep nested structure (#790) @Daniel Suveges
• fix bag in neglog_pvalue_to_mantissa_and_exponent (#795) @Yakov
• [safe_array_union] allow for sorting nested structs (#793) @Szymon Szyszkowski
• remove study_index_path from coloc step (#791) @Szymon Szyszkowski
• [vep_parser] use nested schema for insilico predictors (#789) @Szymon Szyszkowski
• clean unused study_locus step parameter (#786) @David Ochoa
• [finngen_study_index] improved tests for finngen study index (#776) @Szymon Szyszkowski
• remove n_eff check from qc_step (#785) @Yakov
• small qc flag fixes (#784) @Yakov
• [ld clumping] a revised logic allows a more accurate clumping (#772) @Daniel Suveges
• [effect harmonisation] addressing beta harmonisation bug (#762) @Daniel Suveges
• add condition to eQTL study index and schema (#770) @Vivien Ho
• prevent multiple credible filters to override spark plan (#766) @David Ochoa
• multiple fixes after debugging and test runs (#760) @Kirill Tsukanov
• removing old functions (#752) @Yakov
• validation name mapping (#753) @Szymon Szyszkowski
• [finngen_r11] preserve all studyIds (#747) @Szymon Szyszkowski
• remove finngen prefix from credible set (#746) @Szymon Szyszkowski
• adding carma_tau parameter to susie_finemapper (#743) @Yakov
• using h4 instead of log2(h4/h3) (#740) @Daniel-Considine
• revert recursiveFileLookup to False (#738) @Szymon Szyszkowski
• update cluster creation command (#739) @Szymon Szyszkowski
• updating config paths and fine-mapping methods (#725) @Daniel-Considine
• change config params to match new name (#721) @Szymon Szyszkowski

📖 Documentation

• fix broken refs (#768) @David Ochoa
• macos fix for some functions (#729) @Daniel-Considine

♻️ Refactor

• finemapping method enum (#897) @David Ochoa
• [convert to vcf] allow multiple input sources (#891) @Szymon Szyszkowski
• [vep_parser] store consequence to impact score as a project config (#811) @Irene López Santiago
• generalise the harmonisation pipeline (#755) @Kirill Tsukanov
• generalise per-chromosome processing (#754) @Kirill Tsukanov

⚡️ Performance

• quickly build a Docker image for every branch (#773) @Kirill Tsukanov

✅ Test

• skip fetch_coordinates_from_rsids (#850) @Irene López Santiago

🏗 Build

• [deps-dev] bump ruff from 0.7.1 to 0.8.1 (#936) @dependabot[bot]
• [deps-dev] bump ipython from 8.29.0 to 8.30.0 (#937) @dependabot[bot]
• [deps-dev] bump pytest-cov from 5.0.0 to 6.0.0 (#893) @dependabot[bot]
• [deps-dev] bump mypy from 1.12.1 to 1.13.0 (#884) @dependabot[bot]
• [deps-dev] bump ipython from 8.28.0 to 8.29.0 (#883) @dependabot[bot]
• [deps-dev] bump ruff from 0.6.1 to 0.7.0 (#864) @dependabot[bot]
• [deps-dev] bump mypy from 1.11.0 to 1.12.1 (#865) @dependabot[bot]
• [deps-dev] bump mkdocstrings-python from 1.11.1 to 1.12.1 (#842) @dependabot[bot]
• [deps-dev] bump pyparsing from 3.1.2 to 3.2.0 (#836) @dependabot[bot]
• [deps-dev] bump mkdocs-git-committers-plugin-2 from 2.3.0 to 2.4.1 (#818) @dependabot[bot]
• [deps-dev] bump pymdown-extensions from 10.10.1 to 10.11.2 (#815) @dependabot[bot]
• [deps-dev] bump pre-commit from 3.8.0 to 4.0.0 (#820) @dependabot[bot]
• [deps-dev] bump ipython from 8.27.0 to 8.28.0 (#819) @dependabot[bot]
• updated precommits including adjustments to docstrings (#787) @David Ochoa
• [deps-dev] bump pymdown-extensions from 10.9 to 10.10.1 (#781) @dependabot[bot]
• [deps] bump wandb from 0.17.2 to 0.18.0 (#763) @dependabot[bot]
• [deps-dev] bump mkdocstrings-python from 1.10.5 to 1.11.1 (#749) @dependabot[bot]
• [deps-dev] bump deptry from 0.19.1 to 0.20.0 (#742) @dependabot[bot]
• [deps-dev] bump ipython from 8.26.0 to 8.27.0 (#741) @dependabot[bot]
• [deps-dev] bump pre-commit from 3.7.1 to 3.8.0 (#719) @dependabot[bot]
• [deps-dev] bump lxml from 5.2.2 to 5.3.0 (#727) @dependabot[bot]
• [deps-dev] bump deptry from 0.18.0 to 0.19.1 (#728) @dependabot[bot]
• [deps-dev] bump ruff from 0.5.1 to 0.6.1 (#732) @dependabot[bot]
• [deps-dev] bump deptry from 0.17.0 to 0.18.0 (#723) @dependabot[bot]
• [deps-dev] bump pymdown-extensions from 10.8.1 to 10.9 (#720) @dependabot[bot]

👷‍♂️ Ci

• configure java v8 (#840) @Irene López Santiago

🚀 Chore

• [vep] Ensembl version update (#931) @Daniel Suveges
• [gnomad] updating GnomAD version to 4.1 from 4.0 + using joint frequencies (#929) @Daniel Suveges
• pre-commit autoupdate (#918) @pre-commit-ci[bot]
• pre-commit autoupdate (#898) @pre-commit-ci[bot]
• [deps] bump codecov/codecov-action from 4 to 5 (#916) @dependabot[bot]
• validate chromosome (#906) @Daniel Suveges
• [l2g] parametrise score threshold when writing predictions (#907) @Irene López Santiago
• add hf_model_commit_message to LocusToGeneStep (#905) @Irene López Santiago
• pre-commit autoupdate (#885) @pre-commit-ci[bot]
• add chromosome validation (#869) @Yakov
• pre-commit autoupdate (#866) @pre-commit-ci[bot]
• [coloc] changing the content of numberColocalisingVariants field (#857) @Daniel Suveges
• adding logging even when no CS in locus (#848) @Yakov
• remove h4/h3 ratio (#829) @Yakov
• adding priors to coloc step (#830) @Yakov
• make the lb clumping ingest the partitionned data (#806) @Szymon Szyszkowski
• drop redundant parameter (#802) @Szymon Szyszkowski
• pre-commit autoupdate (#724) @pre-commit-ci[bot]
• pre-commit autoupdate (#715) @pre-commit-ci[bot]