cada-prio


Namecada-prio JSON
Version 0.6.1 PyPI version JSON
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home_pagehttps://github.com/bihealth/cada-prio
SummaryPhenotype-based prioritization of variants with CADA
upload_time2023-11-16 07:38:28
maintainer
docs_urlNone
authorManuel Holtgrewe
requires_python>=3.6
licenseMIT license
keywords cada
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls. 
            [![CI](https://github.com/bihealth/cada-prio/actions/workflows/main.yml/badge.svg?branch=main)](https://github.com/bihealth/cada-prio/actions/workflows/main.yml)
[![codecov](https://codecov.io/gh/bihealth/cada-prio/graph/badge.svg?token=HIBwaG4eYM)](https://codecov.io/gh/bihealth/cada-prio)
[![Documentation Status](https://readthedocs.org/projects/cada-prio/badge/?version=latest)](https://cada-prio.readthedocs.io/en/latest/?badge=latest)
[![Pypi](https://img.shields.io/pypi/pyversions/cada-prio.svg)](https://pypi.org/project/cada-prio)

# CADA: The Next Generation

This is a re-implementation of the [CADA](https://github.com/Chengyao-Peng/CADA) method for phenotype-similarity prioritization.

- Free software: MIT license
- Documentation: https://cada-prio.readthedocs.io/en/latest/
- Discussion Forum: https://github.com/bihealth/cada-prio/discussions
- Bug Reports: https://github.com/bihealth/cada-prio/issues

## Running Hyperparameter Tuning

Install with `tune` feature enabled:

```
pip install cada-prio[tune]
```

Run tuning, e.g., on the "classic" model.
Thanks to [optuna](https://optuna.org/), you can run this in parallel as long as the database is shared.
Each run will use 4 CPUs in the example below and perform 1 trial.

```
cada-prio tune run-optuna \
    sqlite:///local_data/cada-tune.sqlite \
    --path-hgnc-json data/classic/hgnc_complete_set.json \
    --path-hpo-genes-to-phenotype data/classic/genes_to_phenotype.all_source_all_freqs_etc.txt \
    --path-hpo-obo data/classic/hp.obo \
    --path-clinvar-phenotype-links data/classic/cases_train.jsonl \
    --path-validation-links data/classic/cases_validate.jsonl \
    --n-trials 1 \
    --cpus=4
```

## Managing GitHub Project with Terraform

```
# export GITHUB_OWNER=bihealth
# export GITHUB_TOKEN=ghp_<thetoken>

# cd utils/terraform

# terraform init
# terraform import github_repository.cada-prio cada-prio
# terraform validate
# terraform fmt
# terraform plan
# terraform apply
```


# Changelog

### [0.6.1](https://www.github.com/bihealth/cada-prio/compare/v0.6.0...v0.6.1) (2023-11-16)


### Bug Fixes

* pinning python to 3.11 for build so we have setuptools ([#36](https://www.github.com/bihealth/cada-prio/issues/36)) ([54d4e8c](https://www.github.com/bihealth/cada-prio/commit/54d4e8c4be8bdd7ad6b9f839b22a798b5f527d27))

## [0.6.0](https://www.github.com/bihealth/cada-prio/compare/v0.5.0...v0.6.0) (2023-11-16)


### Features

* adding API prefix, OpenAPI and docs to REST server ([#35](https://www.github.com/bihealth/cada-prio/issues/35)) ([1a2f605](https://www.github.com/bihealth/cada-prio/commit/1a2f605bbaa28ed511b117efa04de256dcff149d))
* adding classic and current model ([#25](https://www.github.com/bihealth/cada-prio/issues/25)) ([44ddf24](https://www.github.com/bihealth/cada-prio/commit/44ddf24abf939eed8ad56b80cb1e90f60846a390))

## [0.5.0](https://www.github.com/bihealth/cada-prio/compare/v0.4.0...v0.5.0) (2023-09-18)


### Features

* adding "tune run-optuna" command ([#23](https://www.github.com/bihealth/cada-prio/issues/23)) ([6cc753b](https://www.github.com/bihealth/cada-prio/commit/6cc753b3b4f92aa75d961c3cf314e097d174ede0))
* re-useable implementation of "tune train-eval" ([#21](https://www.github.com/bihealth/cada-prio/issues/21)) ([c80c4bf](https://www.github.com/bihealth/cada-prio/commit/c80c4bf1d69ff83bcb84b949cf3383746580a12d))

## [0.4.0](https://www.github.com/bihealth/cada-prio/compare/v0.3.1...v0.4.0) (2023-09-14)


### Features

* adding dump-graph to cli ([#18](https://www.github.com/bihealth/cada-prio/issues/18)) ([3aace31](https://www.github.com/bihealth/cada-prio/commit/3aace31166ddbd4357ae32283b6514a21404e0ef))
* adding param-opt command with single parameter evaluation ([#20](https://www.github.com/bihealth/cada-prio/issues/20)) ([83141c6](https://www.github.com/bihealth/cada-prio/commit/83141c6c4afe6efffc51fcde1ebdc92b5b3d0fbf))
* allow running with legacy model/graph data ([#16](https://www.github.com/bihealth/cada-prio/issues/16)) ([9d3cc7c](https://www.github.com/bihealth/cada-prio/commit/9d3cc7cea6efeac82b41fe11dfc9527ab4fe2913))
* embedding parameters can be provided via CLI and contains seeds ([#19](https://www.github.com/bihealth/cada-prio/issues/19)) ([bbd5d86](https://www.github.com/bihealth/cada-prio/commit/bbd5d86e879db94240093c20145b1c4c45edc69e))

### [0.3.1](https://www.github.com/bihealth/cada-prio/compare/v0.3.0...v0.3.1) (2023-09-13)


### Bug Fixes

* add missing line endings to hgnc_info.jsonl ([#13](https://www.github.com/bihealth/cada-prio/issues/13)) ([aa14b9b](https://www.github.com/bihealth/cada-prio/commit/aa14b9b948a0e9512c57567de2acaa65e9b132bc))
* properly parsing comma-separated list on REST API ([#14](https://www.github.com/bihealth/cada-prio/issues/14)) ([97fdfee](https://www.github.com/bihealth/cada-prio/commit/97fdfeee118d2e4985ca71433617fd9c470d0b49))

## [0.3.0](https://www.github.com/bihealth/cada-prio/compare/v0.2.1...v0.3.0) (2023-09-11)


### Features

* also adding gene-to-phen edges from HPO ([#9](https://www.github.com/bihealth/cada-prio/issues/9)) ([d5a8337](https://www.github.com/bihealth/cada-prio/commit/d5a833774b1488fb7e1f0650692aab2c3f753144))

### [0.2.1](https://www.github.com/bihealth/cada-prio/compare/v0.2.0...v0.2.1) (2023-09-08)


### Bug Fixes

* removing spurious debug print statement ([#7](https://www.github.com/bihealth/cada-prio/issues/7)) ([98e7443](https://www.github.com/bihealth/cada-prio/commit/98e74433001872517a4904bbe85fd021cc4ad613))

## [0.2.0](https://www.github.com/bihealth/cada-prio/compare/v0.1.0...v0.2.0) (2023-09-08)


### Features

* gene to phenotype links file can be gziped ([#5](https://www.github.com/bihealth/cada-prio/issues/5)) ([66c48bf](https://www.github.com/bihealth/cada-prio/commit/66c48bf98c8bd73f8227c7cbd5687b4e74577ef8))

## 0.1.0 (2023-09-07)


### Features

* adding REST API server for prediction ([#4](https://www.github.com/bihealth/cada-prio/issues/4)) ([8bb7516](https://www.github.com/bihealth/cada-prio/commit/8bb75161097529932f371925fe860290098f0885))
* initial training implementation ([#1](https://www.github.com/bihealth/cada-prio/issues/1)) ([10d3a7c](https://www.github.com/bihealth/cada-prio/commit/10d3a7cb356b50a89fd8b1226ad66932dd5542f3))
* prioritization prediction with model ([#3](https://www.github.com/bihealth/cada-prio/issues/3)) ([48d504c](https://www.github.com/bihealth/cada-prio/commit/48d504c0bc373e1ae312773fa70a5a2e04d8dbed))

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with `tune` feature enabled:\n\n```\npip install cada-prio[tune]\n```\n\nRun tuning, e.g., on the \"classic\" model.\nThanks to [optuna](https://optuna.org/), you can run this in parallel as long as the database is shared.\nEach run will use 4 CPUs in the example below and perform 1 trial.\n\n```\ncada-prio tune run-optuna \\\n    sqlite:///local_data/cada-tune.sqlite \\\n    --path-hgnc-json data/classic/hgnc_complete_set.json \\\n    --path-hpo-genes-to-phenotype data/classic/genes_to_phenotype.all_source_all_freqs_etc.txt \\\n    --path-hpo-obo data/classic/hp.obo \\\n    --path-clinvar-phenotype-links data/classic/cases_train.jsonl \\\n    --path-validation-links data/classic/cases_validate.jsonl \\\n    --n-trials 1 \\\n    --cpus=4\n```\n\n## Managing GitHub Project with Terraform\n\n```\n# export GITHUB_OWNER=bihealth\n# export GITHUB_TOKEN=ghp_<thetoken>\n\n# cd utils/terraform\n\n# terraform init\n# terraform import github_repository.cada-prio cada-prio\n# terraform validate\n# terraform fmt\n# terraform plan\n# terraform apply\n```\n\n\n# Changelog\n\n### [0.6.1](https://www.github.com/bihealth/cada-prio/compare/v0.6.0...v0.6.1) (2023-11-16)\n\n\n### Bug Fixes\n\n* pinning python to 3.11 for build so we have setuptools ([#36](https://www.github.com/bihealth/cada-prio/issues/36)) ([54d4e8c](https://www.github.com/bihealth/cada-prio/commit/54d4e8c4be8bdd7ad6b9f839b22a798b5f527d27))\n\n## [0.6.0](https://www.github.com/bihealth/cada-prio/compare/v0.5.0...v0.6.0) (2023-11-16)\n\n\n### Features\n\n* adding API prefix, OpenAPI and docs to REST server ([#35](https://www.github.com/bihealth/cada-prio/issues/35)) ([1a2f605](https://www.github.com/bihealth/cada-prio/commit/1a2f605bbaa28ed511b117efa04de256dcff149d))\n* adding classic and current model ([#25](https://www.github.com/bihealth/cada-prio/issues/25)) ([44ddf24](https://www.github.com/bihealth/cada-prio/commit/44ddf24abf939eed8ad56b80cb1e90f60846a390))\n\n## [0.5.0](https://www.github.com/bihealth/cada-prio/compare/v0.4.0...v0.5.0) (2023-09-18)\n\n\n### Features\n\n* adding \"tune run-optuna\" command ([#23](https://www.github.com/bihealth/cada-prio/issues/23)) ([6cc753b](https://www.github.com/bihealth/cada-prio/commit/6cc753b3b4f92aa75d961c3cf314e097d174ede0))\n* re-useable implementation of \"tune train-eval\" ([#21](https://www.github.com/bihealth/cada-prio/issues/21)) ([c80c4bf](https://www.github.com/bihealth/cada-prio/commit/c80c4bf1d69ff83bcb84b949cf3383746580a12d))\n\n## [0.4.0](https://www.github.com/bihealth/cada-prio/compare/v0.3.1...v0.4.0) (2023-09-14)\n\n\n### Features\n\n* adding dump-graph to cli ([#18](https://www.github.com/bihealth/cada-prio/issues/18)) ([3aace31](https://www.github.com/bihealth/cada-prio/commit/3aace31166ddbd4357ae32283b6514a21404e0ef))\n* adding param-opt command with single parameter evaluation ([#20](https://www.github.com/bihealth/cada-prio/issues/20)) ([83141c6](https://www.github.com/bihealth/cada-prio/commit/83141c6c4afe6efffc51fcde1ebdc92b5b3d0fbf))\n* allow running with legacy model/graph data ([#16](https://www.github.com/bihealth/cada-prio/issues/16)) ([9d3cc7c](https://www.github.com/bihealth/cada-prio/commit/9d3cc7cea6efeac82b41fe11dfc9527ab4fe2913))\n* embedding parameters can be provided via CLI and contains seeds ([#19](https://www.github.com/bihealth/cada-prio/issues/19)) ([bbd5d86](https://www.github.com/bihealth/cada-prio/commit/bbd5d86e879db94240093c20145b1c4c45edc69e))\n\n### [0.3.1](https://www.github.com/bihealth/cada-prio/compare/v0.3.0...v0.3.1) (2023-09-13)\n\n\n### Bug Fixes\n\n* add missing line endings to hgnc_info.jsonl ([#13](https://www.github.com/bihealth/cada-prio/issues/13)) ([aa14b9b](https://www.github.com/bihealth/cada-prio/commit/aa14b9b948a0e9512c57567de2acaa65e9b132bc))\n* properly parsing comma-separated list on REST API ([#14](https://www.github.com/bihealth/cada-prio/issues/14)) ([97fdfee](https://www.github.com/bihealth/cada-prio/commit/97fdfeee118d2e4985ca71433617fd9c470d0b49))\n\n## [0.3.0](https://www.github.com/bihealth/cada-prio/compare/v0.2.1...v0.3.0) (2023-09-11)\n\n\n### Features\n\n* also adding gene-to-phen edges from HPO ([#9](https://www.github.com/bihealth/cada-prio/issues/9)) ([d5a8337](https://www.github.com/bihealth/cada-prio/commit/d5a833774b1488fb7e1f0650692aab2c3f753144))\n\n### [0.2.1](https://www.github.com/bihealth/cada-prio/compare/v0.2.0...v0.2.1) (2023-09-08)\n\n\n### Bug Fixes\n\n* removing spurious debug print statement ([#7](https://www.github.com/bihealth/cada-prio/issues/7)) ([98e7443](https://www.github.com/bihealth/cada-prio/commit/98e74433001872517a4904bbe85fd021cc4ad613))\n\n## [0.2.0](https://www.github.com/bihealth/cada-prio/compare/v0.1.0...v0.2.0) (2023-09-08)\n\n\n### Features\n\n* gene to phenotype links file can be gziped ([#5](https://www.github.com/bihealth/cada-prio/issues/5)) 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Manuel Holtgrewe
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