Filters¶
Filters to supplement pybel.struct.filters
.
Node filters to supplement pybel.struct.filters.node_filters
.
-
pybel_tools.filters.node_filters.
summarize_node_filter
(graph, node_filters)[source]¶ Print a summary of the number of nodes passing a given set of filters.
-
pybel_tools.filters.node_filters.
node_inclusion_filter_builder
(nodes)[source]¶ Build a filter that only passes on nodes in the given list.
-
pybel_tools.filters.node_filters.
node_exclusion_filter_builder
(nodes)[source]¶ Build a filter that fails on nodes in the given list.
-
pybel_tools.filters.node_filters.
function_inclusion_filter_builder
(func)[source]¶ Build a filter that only passes on nodes of the given function(s).
-
pybel_tools.filters.node_filters.
function_exclusion_filter_builder
(func)[source]¶ Build a filter that fails on nodes of the given function(s).
-
pybel_tools.filters.node_filters.
function_namespace_inclusion_builder
(func, namespace)[source]¶ Build a filter function for matching the given BEL function with the given namespace or namespaces.
-
pybel_tools.filters.node_filters.
data_contains_key_builder
(key)[source]¶ Build a filter that passes only on nodes that have the given key in their data dictionary.
-
pybel_tools.filters.node_filters.
node_has_label
(_, node)¶ Passes for nodes that have been annotated with a label
- Return type
-
pybel_tools.filters.node_filters.
node_missing_label
(graph, node)¶ Fails for nodes that have been annotated with a label
- Return type
-
pybel_tools.filters.node_filters.
include_pathology_filter
(_, node)¶ A filter that passes for nodes that are
pybel.constants.PATHOLOGY
- Return type
-
pybel_tools.filters.node_filters.
exclude_pathology_filter
(_, node)¶ A filter that fails for nodes that are
pybel.constants.PATHOLOGY
- Return type
-
pybel_tools.filters.node_filters.
variants_of
(graph, node, modifications=None)[source]¶ Returns all variants of the given node.
- Return type
Set
[Protein
]
-
pybel_tools.filters.node_filters.
get_variants_to_controllers
(graph, node, modifications=None)[source]¶ Get a mapping from variants of the given node to all of its upstream controllers.
-
pybel_tools.filters.node_filters.
data_missing_key_builder
(key)[source]¶ Build a filter that passes only on nodes that don’t have the given key in their data dictionary.
-
pybel_tools.filters.node_filters.
build_node_data_search
(key, data_predicate)[source]¶ Build a filter for nodes whose associated data with the given key passes the given predicate.
-
pybel_tools.filters.node_filters.
build_node_key_search
(query, key)[source]¶ Build a node filter for nodes whose values for the given key are superstrings of the query string(s).
Edge filters to supplement pybel.struct.filters.edge_filters
.
-
pybel_tools.filters.edge_filters.
summarize_edge_filter
(graph, edge_predicates)[source]¶ Print a summary of the number of edges passing a given set of filters.
- Return type
None
-
pybel_tools.filters.edge_filters.
build_edge_data_filter
(annotations, partial_match=True)[source]¶ Build a filter that keeps edges whose data dictionaries are super-dictionaries to the given dictionary.
-
pybel_tools.filters.edge_filters.
build_pmid_inclusion_filter
(pmids)[source]¶ Pass for edges with citations whose references are one of the given PubMed identifiers.
-
pybel_tools.filters.edge_filters.
build_pmid_exclusion_filter
(pmids)[source]¶ Fail for edges with citations whose references are one of the given PubMed identifiers.
Pass only for edges with author information that matches one of the given authors.
-
pybel_tools.filters.edge_filters.
build_source_namespace_filter
(namespaces)[source]¶ Pass for edges whose source nodes have the given namespace or one of the given namespaces.
-
pybel_tools.filters.edge_filters.
build_target_namespace_filter
(namespaces)[source]¶ Only passes for edges whose target nodes have the given namespace or one of the given namespaces
-
pybel_tools.filters.edge_filters.
build_annotation_dict_all_filter
(annotations)[source]¶ Build an edge predicate for edges whose annotations are super-dictionaries of the given dictionary.
If no annotations are given, will always evaluate to true.