Utils¶
Methods for various purposes.
-
class
pathme.utils.CallCounted(method)[source]¶ Decorator to determine number of calls for a method.
Init method.
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pathme.utils.parse_id_uri(uri: str) → Tuple[str, str, str, str][source]¶ Get the components of a given uri (with identifier at the last position).
- Parameters
uri – URI
- Returns
prefix (ex: http://rdf.wikipathways.org/…)
- Returns
prefix_namespaces: if there are many namespaces, until the penultimate (ex: …/Pathway/WP22_r97775/…)
- Returns
namespace: if there are many namespaces, the last (ex: …/Interaction/)
- Returns
identifier (ex: …/c562c/)
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pathme.utils.parse_namespace_uri(uri: str) → Tuple[str, str, str][source]¶ Get the prefix and namespace of a given URI (without identifier, only with a namspace at last position).
- Parameters
uri – URI
- Returns
prefix (ex: http://purl.org/dc/terms/…)
- Returns
namespace (ex: …/isPartOf)
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pathme.utils.parse_rdf(path: str, format: Optional[str] = None) → rdflib.graph.Graph[source]¶ Import a queried pathway into a rdflib Graph object.
- Parameters
path – RDF file path
format – RDF file format, default is turtle
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pathme.utils.entry_result_to_dict(entry, **kwargs)[source]¶ Export to a dictionary a SPARQL query result data structure.
- Returns
entries_dict: Dictionary with all the entries id as keys and the entries arguments as values.
- Return type
-
pathme.utils.query_result_to_dict(entries, **kwargs) → Dict[str, Dict[str, Dict[str, str]]][source]¶ Export to a dictionary a SPARQL query result data structure.
- Returns
entries_dict: Dictionary with all the entries id as keys and the entries arguments as values.
- Return type
-
pathme.utils.get_entry_statitics(types_list, primary_type=None, **kwargs)[source]¶ Get types statistics for a pathway entries type (nodes or interactions) set.
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pathme.utils.get_pathway_statitics(nodes_types, edges_types, bel_graph, **kwargs)[source]¶ Calculate pathway statistics.
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pathme.utils.statistics_to_df(all_pathways_statistics)[source]¶ Build a data frame with graph statistics.
- Parameters
all_pathways_statistics (dict) – pathway statistics
- Return type
pandas.DataFrame
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pathme.utils.get_bel_types(path: str)[source]¶ Get BEL node and edge type statistics.
- Parameters
path – path to pickle
- Returns
count of all nodes and edges in a BEL graph
- Return type
-
pathme.utils.get_bel_stats(resource_folder: str)[source]¶ Get all BEL node and edge type statistics.
- Parameters
resource_folder – path to BEL pickles folder
- Returns
count of all nodes and edges in all BEL graphs from one resource
- Return type
-
pathme.utils.get_genes_from_pickles(resource_folder: str, files: List[str], manager) → Dict[str, set][source]¶ Get BEL graph gene set for all pathways in resource.
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pathme.utils.get_kegg_genes_from_pickles(resource_folder, files: List[str], manager) → Dict[str, Set][source]¶ Get BEL graph gene set for all KEGG pathways.
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pathme.utils.get_genes_in_graph(graph: pybel.struct.graph.BELGraph) → Set[str][source]¶ Get BEL graph gene set for a pathway.
- Parameters
graph – BEL Graph
- Returns
BEL graph gene set
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pathme.utils.jaccard_similarity(database_gene_set, bel_genes_set)[source]¶ Get Jaccard similarity for gene sets in database and BEL graphs.
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pathme.utils.make_downloader(url, path, export_path, decompress_file)[source]¶ Make a function that downloads the data for you, or uses a cached version at the given path.