Manager¶
Manager for Bio2BEL Entrez.
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class
bio2bel_entrez.manager.
Manager
(*args, **kwargs)[source]¶ Genes and orthologies.
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namespace_model
¶ alias of
bio2bel_entrez.models.Gene
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get_or_create_species
(taxonomy_id: str, **kwargs) → bio2bel_entrez.models.Species[source]¶ Get or create a Species model.
- Parameters
taxonomy_id – NCBI taxonomy identifier
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get_gene_by_entrez_id
(entrez_id: str) → Optional[bio2bel_entrez.models.Gene][source]¶ Get a gene with the given Entrez Gene identifier, if it exists.
- Parameters
entrez_id – Entrez Gene identifier
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get_genes_by_name
(name: str) → List[bio2bel_entrez.models.Gene][source]¶ Get a list of genes with the given name (case insensitive).
- Parameters
name – A gene name
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get_gene_by_rgd_name
(name: str) → Optional[bio2bel_entrez.models.Gene][source]¶ Get a gene by its RGD name.
- Parameters
name – RGD gene symbol
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get_gene_by_mgi_name
(name: str) → Optional[bio2bel_entrez.models.Gene][source]¶ Get a gene by its MGI name.
- Parameters
name – MGI gene symbol
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get_gene_by_hgnc_name
(name: str) → Optional[bio2bel_entrez.models.Gene][source]¶ Get a gene by its HGNC gene symbol.
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get_or_create_gene
(entrez_id: str, **kwargs) → bio2bel_entrez.models.Gene[source]¶ Get or create a Gene model.
- Parameters
entrez_id – Entrez Gene identifier
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get_or_create_homologene
(homologene_id: str, **kwargs) → bio2bel_entrez.models.Homologene[source]¶ Get or create a HomoloGene model.
- Parameters
homologene_id – HomoloGene Gene identifier
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populate_homologene
(url=None, cache=True, force_download=False, tax_id_filter=None) → None[source]¶ Populate the database.
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populate_gene_info
(url: Optional[str] = None, cache: bool = True, force_download: bool = False, interval: Optional[int] = None, tax_id_filter: Iterable[str] = None)[source]¶ Populate the database.
- Parameters
url – A custom url to download
interval – The number of records to commit at a time
cache – If true, the data is downloaded to the file system, else it is loaded from the internet
force_download – If true, overwrites a previously cached file
tax_id_filter – Species to keep
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populate
(gene_info_url: Optional[str] = None, interval: Optional[int] = None, tax_id_filter: Iterable[str] = ('9606', '10090', '10116', '7227', '4932', '6239', '7955', '9913', '9615'), homologene_url: Optional[str] = None)[source]¶ Populate the database.
- Parameters
gene_info_url – A custom url to download
interval – The number of records to commit at a time
tax_id_filter – Species to keep. Defaults to 9606 (human), 10090 (mouse), 10116 (rat), 7227 (fly), and 4932 (yeast). Explicitly set to None to get all taxonomies.
homologene_url – A custom url to download
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lookup_node
(node: pybel.dsl.node_classes.BaseEntity) → Optional[bio2bel_entrez.models.Gene][source]¶ Look up a gene from a PyBEL data dictionary.
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iter_genes
(graph: pybel.struct.graph.BELGraph, use_tqdm: bool = False) → Iterable[Tuple[pybel.dsl.node_classes.BaseEntity, bio2bel_entrez.models.Gene]][source]¶ Iterate over genes in the graph that can be mapped to an Entrez gene.
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normalize_genes
(graph: pybel.struct.graph.BELGraph, use_tqdm: bool = False) → None[source]¶ Add identifiers to all Entrez genes.
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enrich_genes_with_homologenes
(graph: pybel.struct.graph.BELGraph) → None[source]¶ Enrich the nodes in a graph with their HomoloGene parents.
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enrich_equivalences
(graph: pybel.struct.graph.BELGraph) → None[source]¶ Add equivalent node information.
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enrich_orthologies
(graph: pybel.struct.graph.BELGraph) → None[source]¶ Add ortholog relationships to graph.
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add_homologene_namespace_to_graph
(graph: pybel.struct.graph.BELGraph) → pybel.manager.models.Namespace[source]¶ Add the homologene namespace to the graph.
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