tooluniverse.gwas_tool moduleΒΆ
- class tooluniverse.gwas_tool.BaseTool(tool_config)[source][source]ΒΆ
Bases:
object
- classmethod get_default_config_file()[source][source]ΒΆ
Get the path to the default configuration file for this tool type.
This method uses a robust path resolution strategy that works across different installation scenarios:
Installed packages: Uses importlib.resources for proper package resource access
Development mode: Falls back to file-based path resolution
Legacy Python: Handles importlib.resources and importlib_resources
Override this method in subclasses to specify a custom defaults file.
- Returns:
Path or resource object pointing to the defaults file
- tooluniverse.gwas_tool.register_tool(tool_type_name=None, config=None)[source][source]ΒΆ
Decorator to automatically register tool classes and their configs.
- Usage:
@register_tool(βCustomToolNameβ, config={β¦}) class MyTool:
pass
- class tooluniverse.gwas_tool.GWASRESTTool(tool_config)[source][source]ΒΆ
Bases:
BaseTool
Base class for GWAS Catalog REST API tools.
- class tooluniverse.gwas_tool.GWASAssociationSearch(tool_config)[source][source]ΒΆ
Bases:
GWASRESTTool
Search for GWAS associations by various criteria.
- class tooluniverse.gwas_tool.GWASStudySearch(tool_config)[source][source]ΒΆ
Bases:
GWASRESTTool
Search for GWAS studies by various criteria.
- class tooluniverse.gwas_tool.GWASSNPSearch(tool_config)[source][source]ΒΆ
Bases:
GWASRESTTool
Search for GWAS single nucleotide polymorphisms (SNPs).
- class tooluniverse.gwas_tool.GWASAssociationByID(tool_config)[source][source]ΒΆ
Bases:
GWASRESTTool
Get a specific GWAS association by its ID.
- class tooluniverse.gwas_tool.GWASStudyByID(tool_config)[source][source]ΒΆ
Bases:
GWASRESTTool
Get a specific GWAS study by its ID.
- class tooluniverse.gwas_tool.GWASSNPByID(tool_config)[source][source]ΒΆ
Bases:
GWASRESTTool
Get a specific GWAS SNP by its rs ID.
- class tooluniverse.gwas_tool.GWASVariantsForTrait(tool_config)[source][source]ΒΆ
Bases:
GWASRESTTool
Get all variants associated with a specific trait.
- class tooluniverse.gwas_tool.GWASAssociationsForTrait(tool_config)[source][source]ΒΆ
Bases:
GWASRESTTool
Get all associations for a specific trait, sorted by p-value.
- class tooluniverse.gwas_tool.GWASAssociationsForSNP(tool_config)[source][source]ΒΆ
Bases:
GWASRESTTool
Get all associations for a specific SNP.
- class tooluniverse.gwas_tool.GWASStudiesForTrait(tool_config)[source][source]ΒΆ
Bases:
GWASRESTTool
Get studies for a specific trait with optional filters.
- class tooluniverse.gwas_tool.GWASSNPsForGene(tool_config)[source][source]ΒΆ
Bases:
GWASRESTTool
Get SNPs mapped to a specific gene.