kg_covid_19.transform_utils.sars_cov_2_gene_annot package

Submodules

kg_covid_19.transform_utils.sars_cov_2_gene_annot.sars_cov_2_gene_annot module

class kg_covid_19.transform_utils.sars_cov_2_gene_annot.sars_cov_2_gene_annot.SARSCoV2GeneAnnot(input_dir: Optional[str] = None, output_dir: str = None)

Bases: kg_covid_19.transform_utils.transform.Transform

gpa_to_edge_data(rec: dict) → list

given a parsed gpa entry, return an edge with the annotations

Parameters

rec – record from gpa iterator

Returns

gpi_to_gene_node_data(rec: dict) → list

given a parsed gpi entry, return a node that can be passed to write_node_edge_item()

Parameters

rec – record from gpi iterator

Returns

list of node items, one for each thing in self.node_header

run(data_file: str = None)

Module contents

class kg_covid_19.transform_utils.sars_cov_2_gene_annot.SARSCoV2GeneAnnot(input_dir: Optional[str] = None, output_dir: str = None)

Bases: kg_covid_19.transform_utils.transform.Transform

gpa_to_edge_data(rec: dict) → list

given a parsed gpa entry, return an edge with the annotations

Parameters

rec – record from gpa iterator

Returns

gpi_to_gene_node_data(rec: dict) → list

given a parsed gpi entry, return a node that can be passed to write_node_edge_item()

Parameters

rec – record from gpi iterator

Returns

list of node items, one for each thing in self.node_header

run(data_file: str = None)