ncbi_gene_pyobo package

Subpackages

• ncbi_gene_pyobo.transform_utils package
  • Submodules
  • ncbi_gene_pyobo.transform_utils.ontology_transform module
    • OntologyTransform
      • OntologyTransform.parse()
      • OntologyTransform.run()
  • ncbi_gene_pyobo.transform_utils.transform module
    • Transform
  • Module contents
    • OntologyTransform
      • OntologyTransform.parse()
      • OntologyTransform.run()

Submodules

ncbi_gene_pyobo.cli module

Command line interface for ncbi-gene-pyobo.

ncbi_gene_pyobo.cli.get_obo(force=False)

Get Entrez as OBO.

Return type:

Obo

ncbi_gene_pyobo.constants module

Constants used in the project.

ncbi_gene_pyobo.duckdb_utils module

Convert the NCBI Gene data to a DuckDB database and export in KGX format.

ncbi_gene_pyobo.duckdb_utils.ncbigene_2_kgx()

Convert the NCBI Gene data to a DuckDB database and export in KGX format.

ncbi_gene_pyobo.transform module

Transform module.

ncbi_gene_pyobo.transform.transform(input_dir, output_dir, sources=None)

Transform based on resource and class declared in DATA_SOURCES.

Parameters:

• input_dir (Optional[Path]) – A string pointing to the directory to import data from.

• output_dir (Optional[Path]) – A string pointing to the directory to output data to.

• sources (Optional[List[str]]) – A list of sources to transform.

Return type:

None

Module contents

ncbi-gene-pyobo package.