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"apache-airflow[postgres]", "apache-airflow[presto]", "apache-airflow[trino]", "apache-airflow[vertica]"] amazon = ["apache-airflow-providers-amazon"] apache-atlas = ["atlasclient (>=0.1.2)"] apache-beam = ["apache-airflow-providers-apache-beam"] @@ -290,7 +292,7 @@ apache-drill = ["apache-airflow-providers-apache-drill"] apache-druid = ["apache-airflow-providers-apache-druid"] apache-flink = ["apache-airflow-providers-apache-flink"] apache-hdfs = ["apache-airflow-providers-apache-hdfs"] -apache-hive = ["apache-airflow-providers-apache-hive (>=5.1.0)"] +apache-hive = ["apache-airflow-providers-apache-hive"] apache-impala = ["apache-airflow-providers-apache-impala"] apache-kafka = ["apache-airflow-providers-apache-kafka"] apache-kylin = ["apache-airflow-providers-apache-kylin"] @@ -303,53 +305,50 @@ apprise = ["apache-airflow-providers-apprise"] arangodb = ["apache-airflow-providers-arangodb"] asana = ["apache-airflow-providers-asana"] async = ["eventlet (>=0.33.3)", "gevent (>=0.13)", "greenlet (>=0.4.9)"] -atlas = ["apache-airflow-providers-apache-atlas"] +atlas = ["apache-airflow[apache-atlas]"] atlassian-jira = ["apache-airflow-providers-atlassian-jira"] -aws = ["apache-airflow-providers-amazon"] -azure = ["apache-airflow-providers-microsoft-azure"] -cassandra = ["apache-airflow-providers-apache-cassandra"] -celery = ["apache-airflow (>=2.6.0)", "apache-airflow-providers-celery", "celery (>=5.3.0,!=5.3.2,!=5.3.3,<6)", "flower (>=1.0.0)", "google-re2 (>=1.0)"] +aws = ["apache-airflow[amazon]"] +azure = ["apache-airflow[microsoft-azure]"] +cassandra = ["apache-airflow[apache-cassandra]"] +celery = ["apache-airflow-providers-celery"] cgroups = ["cgroupspy (>=0.2.2)"] cloudant = ["apache-airflow-providers-cloudant"] -cncf-kubernetes = ["aiofiles (>=23.2.0)", "apache-airflow (>=2.6.0)", "apache-airflow-providers-cncf-kubernetes", "asgiref (>=3.5.2)", "cryptography (>=2.0.0)", "google-re2 (>=1.0)", "kubernetes (>=21.7.0,<24)", "kubernetes-asyncio (>=18.20.1,<25)"] +cncf-kubernetes = ["apache-airflow-providers-cncf-kubernetes"] cohere = ["apache-airflow-providers-cohere"] common-io = ["apache-airflow-providers-common-io"] common-sql = ["apache-airflow-providers-common-sql"] databricks = ["apache-airflow-providers-databricks"] datadog = ["apache-airflow-providers-datadog"] dbt-cloud = ["apache-airflow-providers-dbt-cloud"] -deprecated-api = ["requests (>=2.26.0)"] -devel = ["aiobotocore (>=2.1.1)", "aioresponses", "apache-airflow (>=2.6.0)", "apache-airflow-providers-common-sql", "astroid (>=2.12.3,<3.0)", "aws-xray-sdk", "backports.zoneinfo (>=0.2.1)", "bcrypt (>=2.0.0)", "beautifulsoup4 (>=4.7.1)", "black", "blinker", "cgroupspy (>=0.2.2)", "checksumdir", "click (>=8.0)", "click (>=8.0,!=8.1.4,!=8.1.5)", "coverage (>=7.2)", "cryptography (>=2.0.0)", "deltalake (>=0.12.0)", "docutils (<0.17.0)", "duckdb (>=0.9.0)", "eralchemy2", "filelock", "flask-bcrypt (>=0.7.1)", "gitpython", "ipdb", "kubernetes (>=21.7.0,<24)", "mongomock", 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"virtualenv", "wheel (>=0.42.0)", "yamllint (>=1.33.0)"] dingding = ["apache-airflow-providers-dingding"] discord = ["apache-airflow-providers-discord"] -doc = ["astroid (>=2.12.3,<3.0)", "checksumdir", "click (>=8.0,!=8.1.4,!=8.1.5)", "docutils (<0.17.0)", "eralchemy2", "sphinx (>=5.2.0)", "sphinx-airflow-theme", "sphinx-argparse (>=0.1.13)", "sphinx-autoapi (>=2.0.0)", "sphinx-copybutton", "sphinx-design (>=0.5.0)", "sphinx-jinja (>=2.0)", "sphinx-rtd-theme (>=0.1.6)", "sphinxcontrib-httpdomain (>=1.7.0)", "sphinxcontrib-redoc (>=1.6.0)", "sphinxcontrib-spelling (>=7.3)"] -doc-gen = ["eralchemy2"] docker = ["apache-airflow-providers-docker"] -druid = ["apache-airflow-providers-apache-druid"] +druid = ["apache-airflow[apache-druid]"] elasticsearch = ["apache-airflow-providers-elasticsearch"] exasol = ["apache-airflow-providers-exasol"] +fab = ["apache-airflow-providers-fab"] facebook = ["apache-airflow-providers-facebook"] ftp = ["apache-airflow-providers-ftp"] -gcp = ["apache-airflow-providers-google"] -gcp-api = ["apache-airflow-providers-google"] +gcp = ["apache-airflow[google]"] +gcp-api = ["apache-airflow[google]"] github = ["apache-airflow-providers-github"] -github-enterprise = ["authlib (>=1.0.0)", "flask-appbuilder[oauth] (==4.3.10)"] +github-enterprise = ["apache-airflow[fab]", "authlib (>=1.0.0)"] google = ["apache-airflow-providers-google"] -google-auth = ["authlib (>=1.0.0)", "flask-appbuilder[oauth] (==4.3.10)"] +google-auth = ["apache-airflow[fab]", "authlib (>=1.0.0)"] +graphviz = ["graphviz (>=0.12)"] grpc = ["apache-airflow-providers-grpc"] hashicorp = ["apache-airflow-providers-hashicorp"] -hdfs = ["apache-airflow-providers-apache-hdfs"] -hive = ["apache-airflow-providers-apache-hive"] +hdfs = ["apache-airflow[apache-hdfs]"] +hive = ["apache-airflow[apache-hive]"] http = ["apache-airflow-providers-http"] imap = ["apache-airflow-providers-imap"] influxdb = ["apache-airflow-providers-influxdb"] jdbc = ["apache-airflow-providers-jdbc"] jenkins = ["apache-airflow-providers-jenkins"] kerberos = ["pykerberos (>=1.1.13)", "requests-kerberos (>=0.10.0)", "thrift-sasl (>=0.2.0)"] -kubernetes = ["aiofiles (>=23.2.0)", "apache-airflow (>=2.6.0)", "apache-airflow-providers-cncf-kubernetes", "asgiref (>=3.5.2)", "cryptography (>=2.0.0)", "google-re2 (>=1.0)", "kubernetes (>=21.7.0,<24)", "kubernetes-asyncio (>=18.20.1,<25)"] +kubernetes = ["apache-airflow[cncf-kubernetes]"] ldap = ["ldap3 (>=2.5.1)", "python-ldap"] leveldb = ["plyvel"] microsoft-azure = ["apache-airflow-providers-microsoft-azure"] @@ -357,7 +356,7 @@ microsoft-mssql = ["apache-airflow-providers-microsoft-mssql"] microsoft-psrp = ["apache-airflow-providers-microsoft-psrp"] microsoft-winrm = ["apache-airflow-providers-microsoft-winrm"] mongo = ["apache-airflow-providers-mongo"] -mssql = ["apache-airflow-providers-microsoft-mssql"] +mssql = ["apache-airflow[microsoft-mssql]"] mysql = ["apache-airflow-providers-mysql"] neo4j = ["apache-airflow-providers-neo4j"] odbc = ["apache-airflow-providers-odbc"] @@ -369,17 +368,19 @@ opsgenie = ["apache-airflow-providers-opsgenie"] oracle = ["apache-airflow-providers-oracle"] otel = ["opentelemetry-exporter-prometheus"] pagerduty = ["apache-airflow-providers-pagerduty"] -pandas = ["pandas (>=0.17.1)", "pyarrow (>=9.0.0)", "pyarrow-hotfix"] +pandas = ["pandas (>=1.2.5,<2.2)"] papermill = ["apache-airflow-providers-papermill"] password = ["bcrypt (>=2.0.0)", "flask-bcrypt (>=0.7.1)"] pgvector = ["apache-airflow-providers-pgvector"] pinecone = ["apache-airflow-providers-pinecone"] -pinot = ["apache-airflow-providers-apache-pinot"] +pinot = ["apache-airflow[apache-pinot]"] postgres = ["apache-airflow-providers-postgres"] presto = ["apache-airflow-providers-presto"] +pydantic = ["pydantic (>=2.3.0)"] +qdrant = ["apache-airflow-providers-qdrant"] rabbitmq = ["amqp"] redis = ["apache-airflow-providers-redis"] -s3 = ["apache-airflow-providers-amazon"] +s3 = ["apache-airflow[amazon]"] s3fs = ["s3fs (>=2023.10.0)"] salesforce = ["apache-airflow-providers-salesforce"] samba = ["apache-airflow-providers-samba"] @@ -392,54 +393,93 @@ singularity = ["apache-airflow-providers-singularity"] slack = ["apache-airflow-providers-slack"] smtp = ["apache-airflow-providers-smtp"] snowflake = ["apache-airflow-providers-snowflake"] -spark = ["apache-airflow-providers-apache-spark"] +spark = ["apache-airflow[apache-spark]"] sqlite = ["apache-airflow-providers-sqlite"] ssh = ["apache-airflow-providers-ssh"] statsd = ["statsd (>=3.3.0)"] tableau = ["apache-airflow-providers-tableau"] tabular = ["apache-airflow-providers-tabular"] telegram = ["apache-airflow-providers-telegram"] +teradata = ["apache-airflow-providers-teradata"] trino = ["apache-airflow-providers-trino"] +uv = ["uv (>=0.1.32)"] vertica = ["apache-airflow-providers-vertica"] virtualenv = ["virtualenv"] weaviate = ["apache-airflow-providers-weaviate"] -webhdfs = ["hdfs[avro,dataframe,kerberos] (>=2.0.4)"] -winrm = ["apache-airflow-providers-microsoft-winrm"] +webhdfs = ["apache-airflow[apache-webhdfs]"] +winrm = ["apache-airflow[microsoft-winrm]"] yandex = ["apache-airflow-providers-yandex"] zendesk = ["apache-airflow-providers-zendesk"] +[[package]] +name = "apache-airflow-providers-common-io" +version = "1.3.2" +description = "Provider package apache-airflow-providers-common-io for Apache Airflow" +optional = false +python-versions = "~=3.8" +files = [ + {file = "apache_airflow_providers_common_io-1.3.2-py3-none-any.whl", hash = "sha256:7c0299d8eb2e3fc7b99f522c4d333e2b888edbf47861a8f3e3ae78707ae77aab"}, + {file = "apache_airflow_providers_common_io-1.3.2.tar.gz", hash = "sha256:1212e484a16ad311bcb979e84ad1fa1cc45d7f5ba4dfcbd7978887bd30809e75"}, +] + +[package.dependencies] +apache-airflow = ">=2.8.0" + +[package.extras] +openlineage = ["apache-airflow-providers-openlineage"] + [[package]] name = "apache-airflow-providers-common-sql" -version = "1.8.0" -description = "Provider for Apache Airflow. Implements apache-airflow-providers-common-sql package" +version = "1.14.0" +description = "Provider package apache-airflow-providers-common-sql for Apache Airflow" optional = false python-versions = "~=3.8" files = [ - {file = "apache-airflow-providers-common-sql-1.8.0.tar.gz", hash = "sha256:4d8d99f33f7b5a3e313ef12c5a2f10d1612477ed2e784d0ffb721447e076e3f7"}, - {file = "apache_airflow_providers_common_sql-1.8.0-py3-none-any.whl", hash = "sha256:45117fa38f5a2e83cdb9a8d3bdfdbd602bfdc7a894d087b26e6ebb94df79ec32"}, + {file = "apache_airflow_providers_common_sql-1.14.0-py3-none-any.whl", hash = "sha256:620ba5bf559964159b3faf0bf921e666d1c3bb74ade27daa385f9e9ecd413a1c"}, + {file = "apache_airflow_providers_common_sql-1.14.0.tar.gz", hash = "sha256:6179512edf261ede96adda31a535eec024471a5708a7528d27a4ece72f35783f"}, ] [package.dependencies] -apache-airflow = ">=2.5.0" +apache-airflow = ">=2.7.0" +more-itertools = ">=9.0.0" sqlparse = ">=0.4.2" [package.extras] openlineage = ["apache-airflow-providers-openlineage"] -pandas = ["pandas (>=0.17.1)"] +pandas = ["pandas (>=1.2.5,<2.2)"] + +[[package]] +name = "apache-airflow-providers-fab" +version = "1.1.1" +description = "Provider package apache-airflow-providers-fab for Apache Airflow" +optional = false +python-versions = "~=3.8" +files = [ + {file = "apache_airflow_providers_fab-1.1.1-py3-none-any.whl", hash = "sha256:5d393d209ef432618e1926b019fb7b543d1fc932b592c39b4170779c409a38a5"}, + {file = "apache_airflow_providers_fab-1.1.1.tar.gz", hash = "sha256:60c1722f9985675e65f78c05bca8b4eb708a3140a2ed16d8de2c4cc4a4ecadc3"}, +] + +[package.dependencies] +apache-airflow = ">=2.9.0" +flask = ">=2.2,<2.3" +flask-appbuilder = "4.4.1" +flask-login = ">=0.6.2" +google-re2 = ">=1.0" +jmespath = "*" [[package]] name = "apache-airflow-providers-ftp" -version = "3.6.0" -description = "Provider for Apache Airflow. Implements apache-airflow-providers-ftp package" +version = "3.9.1" +description = "Provider package apache-airflow-providers-ftp for Apache Airflow" optional = false python-versions = "~=3.8" files = [ - {file = "apache-airflow-providers-ftp-3.6.0.tar.gz", hash = "sha256:160f12e9f78ffbcdca4bdffbac93c1f04641fd3f1f7d236c7bfe79cd0a68d14b"}, - {file = "apache_airflow_providers_ftp-3.6.0-py3-none-any.whl", hash = "sha256:03264207293710c3821f5ccd548c5e89a3c5ca7562bc4ff629e6f73d112a71a4"}, + {file = "apache_airflow_providers_ftp-3.9.1-py3-none-any.whl", hash = "sha256:74744b27f356bc42b528605d33a868ed2b4c670a1c90a857fb05402740e6f980"}, + {file = "apache_airflow_providers_ftp-3.9.1.tar.gz", hash = "sha256:b5cc4445a6fabb73f760c678d1b7f1d10586dfc6c9d34746c7462180f1cbb3ce"}, ] [package.dependencies] -apache-airflow = ">=2.5.0" +apache-airflow = ">=2.7.0" [package.extras] openlineage = ["apache-airflow-providers-openlineage"] @@ -538,49 +578,63 @@ trino = ["apache-airflow-providers-trino"] [[package]] name = "apache-airflow-providers-http" -version = "4.6.0" -description = "Provider for Apache Airflow. Implements apache-airflow-providers-http package" +version = "4.11.1" +description = "Provider package apache-airflow-providers-http for Apache Airflow" optional = false python-versions = "~=3.8" files = [ - {file = "apache-airflow-providers-http-4.6.0.tar.gz", hash = "sha256:c9b08782031daa8c18ba62c2c8ae687659968d636fbf6b9fbed488d1fe4f0162"}, - {file = "apache_airflow_providers_http-4.6.0-py3-none-any.whl", hash = "sha256:ca3cf6c209cb27144fd4d676ee5feef96a1ed67002f13bf4a8b74d859ef8b56c"}, + {file = "apache_airflow_providers_http-4.11.1-py3-none-any.whl", hash = "sha256:f8aff8d009d8068654bed6c84c1bf13100ebbda4563c5fdea067047ba85a84bf"}, + {file = "apache_airflow_providers_http-4.11.1.tar.gz", hash = "sha256:401c4c976ca35388574afa85282fa35ed0514a77ef7ca442ea74132b3442a869"}, ] [package.dependencies] -aiohttp = "*" -apache-airflow = ">=2.5.0" +aiohttp = ">=3.9.2" +apache-airflow = ">=2.7.0" asgiref = "*" -requests = ">=2.26.0" -requests-toolbelt = "*" +requests = ">=2.27.0,<3" +requests_toolbelt = "*" [[package]] name = "apache-airflow-providers-imap" -version = "3.4.0" -description = "Provider for Apache Airflow. Implements apache-airflow-providers-imap package" +version = "3.6.1" +description = "Provider package apache-airflow-providers-imap for Apache Airflow" +optional = false +python-versions = "~=3.8" +files = [ + {file = "apache_airflow_providers_imap-3.6.1-py3-none-any.whl", hash = "sha256:1630dfad25a4db28da37ed4cb522674e37d0d981238fdb34ed2933c7f348763a"}, + {file = "apache_airflow_providers_imap-3.6.1.tar.gz", hash = "sha256:20e8052b43f32c3e711cbe0ffe3763cf550ffb06011ed4c57c3e806dd99dfa06"}, +] + +[package.dependencies] +apache-airflow = ">=2.7.0" + +[[package]] +name = "apache-airflow-providers-smtp" +version = "1.7.1" +description = "Provider package apache-airflow-providers-smtp for Apache Airflow" optional = false python-versions = "~=3.8" files = [ - {file = "apache-airflow-providers-imap-3.4.0.tar.gz", hash = "sha256:347f78efa0e1353f90be78244fad0136d7c0cb1af25b9a3ba296d4e31fb53f6c"}, - {file = "apache_airflow_providers_imap-3.4.0-py3-none-any.whl", hash = "sha256:4972793b0dbb25d5372fe1bf174329958075985c0beca013459ec89fcbbca620"}, + {file = "apache_airflow_providers_smtp-1.7.1-py3-none-any.whl", hash = "sha256:eab0910fa1351e58e1e87bb2489084ad5157e33a8752cce3164fd38f4b50c694"}, + {file = "apache_airflow_providers_smtp-1.7.1.tar.gz", hash = "sha256:707c4e2d75ce328693b55429f1f771e00cd2a2d6b52ce14edc20cb6d785be76e"}, ] [package.dependencies] -apache-airflow = ">=2.5.0" +apache-airflow = ">=2.7.0" [[package]] name = "apache-airflow-providers-sqlite" -version = "3.5.0" -description = "Provider for Apache Airflow. Implements apache-airflow-providers-sqlite package" +version = "3.8.1" +description = "Provider package apache-airflow-providers-sqlite for Apache Airflow" optional = false python-versions = "~=3.8" files = [ - {file = "apache-airflow-providers-sqlite-3.5.0.tar.gz", hash = "sha256:6f47c25d7fb026fa8b8b4dc8edfee1491998255048255625716fceaae2c67024"}, - {file = "apache_airflow_providers_sqlite-3.5.0-py3-none-any.whl", hash = "sha256:7baba67c9ddf75b31d8197e22ca491c2e1cf9e4c6306c1788c150b5457c3a182"}, + {file = "apache_airflow_providers_sqlite-3.8.1-py3-none-any.whl", hash = "sha256:be9749275ac266245a2973269842674b10c3ad184790f9f0fd75e76e1d3b2440"}, + {file = "apache_airflow_providers_sqlite-3.8.1.tar.gz", hash = "sha256:b958c5aa725fcf6505c77dc3d600f3c6f9255be5405ea51fa966ae1d85842d3e"}, ] [package.dependencies] -apache-airflow = ">=2.5.0" +apache-airflow = ">=2.7.0" apache-airflow-providers-common-sql = ">=1.3.1" [package.extras] @@ -588,13 +642,13 @@ common-sql = ["apache-airflow-providers-common-sql"] [[package]] name = "apispec" -version = "6.3.0" +version = "6.6.1" description = "A pluggable API specification generator. Currently supports the OpenAPI Specification (f.k.a. the Swagger specification)." optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "apispec-6.3.0-py3-none-any.whl", hash = "sha256:95a0b9355785df998bb0e9b939237a30ee4c7428fd6ef97305eae3da06b9b339"}, - {file = "apispec-6.3.0.tar.gz", hash = "sha256:6cb08d92ce73ff0b3bf46cb2ea5c00d57289b0f279fb0256a3df468182ba5344"}, + {file = "apispec-6.6.1-py3-none-any.whl", hash = "sha256:6460315cb38ac6a2ff42d9e2b8dc0435c37d4428d3abeda96ff97b5dc8eb6b94"}, + {file = "apispec-6.6.1.tar.gz", hash = "sha256:f5caa47cee75fe03b9c50b5594048b4c052eeca2c212e0dac12dbb6175d9a659"}, ] [package.dependencies] @@ -602,34 +656,32 @@ packaging = ">=21.3" PyYAML = {version = ">=3.10", optional = true, markers = "extra == \"yaml\""} [package.extras] -dev = ["PyYAML (>=3.10)", "flake8 (==5.0.4)", "flake8-bugbear (==22.9.23)", "marshmallow (>=3.13.0)", "mypy (==0.982)", "openapi-spec-validator (<0.5)", "prance[osv] (>=0.11)", "pre-commit (>=2.4,<3.0)", "pytest", "tox", "types-PyYAML"] -docs = ["marshmallow (>=3.13.0)", "pyyaml (==6.0)", "sphinx (==5.2.3)", "sphinx-issues (==3.0.1)", "sphinx-rtd-theme (==1.0.0)"] -lint = ["flake8 (==5.0.4)", "flake8-bugbear (==22.9.23)", "mypy (==0.982)", "pre-commit (>=2.4,<3.0)", "types-PyYAML"] +dev = ["apispec[tests]", "pre-commit (>=3.5,<4.0)", "tox"] +docs = ["apispec[marshmallow]", "pyyaml (==6.0.1)", "sphinx (==7.3.7)", "sphinx-issues (==4.1.0)", "sphinx-rtd-theme (==2.0.0)"] marshmallow = ["marshmallow (>=3.18.0)"] -tests = ["PyYAML (>=3.10)", "marshmallow (>=3.13.0)", "openapi-spec-validator (<0.5)", "prance[osv] (>=0.11)", "pytest"] -validation = ["openapi-spec-validator (<0.5)", "prance[osv] (>=0.11)"] +tests = ["apispec[marshmallow,yaml]", "openapi-spec-validator (==0.7.1)", "pytest"] yaml = ["PyYAML (>=3.10)"] [[package]] name = "appnope" -version = "0.1.3" +version = "0.1.4" description = "Disable App Nap on macOS >= 10.9" optional = false -python-versions = "*" +python-versions = ">=3.6" files = [ - 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a/pyproject.toml b/pyproject.toml index c92a56339..c9b3a911d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,6 +33,7 @@ omegaconf = "^2.3.0" typing-extensions = "^4.9.0" scikit-learn = "^1.3.2" pandas = {extras = ["gcp", "parquet"], version = "^2.2.2"} +google-cloud-secret-manager = "^2.20.0" [tool.poetry.dev-dependencies] pre-commit = "^3.7.0" diff --git a/src/gentropy/common/utils.py b/src/gentropy/common/utils.py index 3ec361a50..52be4429f 100644 --- a/src/gentropy/common/utils.py +++ b/src/gentropy/common/utils.py @@ -314,3 +314,21 @@ def get_logsum(arr: NDArray[np.float64]) -> float: themax = np.max(arr) result = themax + np.log(np.sum(np.exp(arr - themax))) return float(result) + + +def access_gcp_secret(secret_id: str, project_id: str) -> str: + """Access GCP secret manager to get the secret value. + + Args: + secret_id (str): ID of the secret + project_id (str): ID of the GCP project + + Returns: + str: secret value + """ + from google.cloud import secretmanager + + client = secretmanager.SecretManagerServiceClient() + name = f"projects/{project_id}/secrets/{secret_id}/versions/latest" + response = client.access_secret_version(name=name) + return response.payload.data.decode("UTF-8") diff --git a/src/gentropy/susie_finemapper.py b/src/gentropy/susie_finemapper.py index cbc024acf..807881a85 100644 --- a/src/gentropy/susie_finemapper.py +++ b/src/gentropy/susie_finemapper.py @@ -23,6 +23,7 @@ from gentropy.common.session import Session from gentropy.common.spark_helpers import neglog_pvalue_to_mantissa_and_exponent +from gentropy.dataset.ld_index import LDIndex from gentropy.dataset.study_index import StudyIndex from gentropy.dataset.study_locus import StudyLocus from gentropy.dataset.summary_statistics import SummaryStatistics @@ -1168,3 +1169,45 @@ def susie_finemapper_one_studylocus_row_v3_dev_ss_gathered( ) return out + + @staticmethod + def credible_set_qc( + cred_sets: StudyLocus, + study_index: StudyIndex, + ld_index: LDIndex, + p_value_threshold: float = 1e-5, + purity_min_r2: float = 0.01, + ) -> StudyLocus: + """Filter credible sets by lead P-value and min-R2 purity, and performs LD clumping. + + Args: + cred_sets (StudyLocus): StudyLocus object with credible sets to filter/clump + study_index (StudyIndex): StudyIndex object + ld_index (LDIndex): LDIndex object + p_value_threshold (float): p-value threshold for filtering credible sets, default is 1e-5 + purity_min_r2 (float): min-R2 purity threshold for filtering credible sets, default is 0.25 + + Returns: + StudyLocus: Credible sets which pass filters and LD clumping. + """ + df = ( + cred_sets.df.withColumn( + "pValue", f.col("pValueMantissa") * f.pow(10, f.col("pValueExponent")) + ) + .filter(f.col("pValue") <= p_value_threshold) + .filter(f.col("purityMinR2") >= purity_min_r2) + .drop("pValue") + ) + cred_sets.df = df + cred_sets = ( + cred_sets.annotate_ld(study_index, ld_index) + .clump() + .filter( + ~f.array_contains( + f.col("qualityControls"), + "Explained by a more significant variant in high LD (clumped)", + ) + ) + ) + + return cred_sets