Index

Symbols

--all pathme_viewer-manage-export-to-tsv command line option --connection <connection> pathme_viewer-manage command line option pathme_viewer-manage-drop command line option pathme_viewer-manage-export-to-tsv command line option pathme_viewer-manage-load command line option pathme_viewer-manage-summarize command line option --debug pathme_viewer-manage-drop command line option --flatten <flatten> pathme_viewer-manage-load command line option --host <host> pathme_viewer-web command line option --kegg_path <kegg_path> pathme_viewer-manage-load command line option --port <port> pathme_viewer-web command line option --reactome_path <reactome_path> pathme_viewer-manage-load command line option --static <static> pathme_viewer-web command line option --template <template> pathme_viewer-web command line option --verbose pathme_viewer-web command line option

--wikipathways_path <wikipathways_path> pathme_viewer-manage-load command line option --yes pathme_viewer-manage-drop command line option pathme_viewer-manage-load command line option -a pathme_viewer-manage-export-to-tsv command line option -c pathme_viewer-manage command line option pathme_viewer-manage-drop command line option pathme_viewer-manage-export-to-tsv command line option pathme_viewer-manage-load command line option pathme_viewer-manage-summarize command line option -f pathme_viewer-manage-load command line option -kp pathme_viewer-manage-load command line option -rp pathme_viewer-manage-load command line option -v pathme_viewer-manage-drop command line option pathme_viewer-web command line option -wp pathme_viewer-manage-load command line option -y pathme_viewer-manage-drop command line option pathme_viewer-manage-load command line option

A

as_bel() (pathme_viewer.models.Pathway method)

authors (pathme_viewer.models.Pathway attribute)

B

blob (pathme_viewer.models.Pathway attribute)

C

contact (pathme_viewer.models.Pathway attribute) count_pathways() (pathme_viewer.manager.Manager method)

count_pathways_by_resource() (pathme_viewer.manager.Manager method) create_all() (pathme_viewer.manager.Manager method) create_pathway() (pathme_viewer.manager.Manager method)

D

delete_all_pathways() (pathme_viewer.manager.Manager method) delete_pathway() (pathme_viewer.manager.Manager method) delete_pathways_from_resource() (pathme_viewer.manager.Manager method)

description (pathme_viewer.models.Pathway attribute) display_name() (pathme_viewer.models.Pathway property) drop_all() (pathme_viewer.manager.Manager method)

G

get_all_pathway_graphs() (pathme_viewer.manager.Manager method) get_all_pathways() (pathme_viewer.manager.Manager method) get_or_create_pathway() (pathme_viewer.manager.Manager method)

get_pathway_by_id() (pathme_viewer.manager.Manager method) get_pathway_by_name() (pathme_viewer.manager.Manager method) get_pathways_from_resource() (pathme_viewer.manager.Manager method)

M

Manager (class in pathme_viewer.manager)

N

name (pathme_viewer.models.Pathway attribute)

number_of_edges (pathme_viewer.models.Pathway attribute) number_of_nodes (pathme_viewer.models.Pathway attribute)

P

pathme_viewer (module) pathme_viewer-manage command line option --connection <connection> -c pathme_viewer-manage-drop command line option --connection <connection> --debug --yes -c -v -y pathme_viewer-manage-export-to-tsv command line option --all --connection <connection> -a -c pathme_viewer-manage-load command line option --connection <connection> --flatten <flatten> --kegg_path <kegg_path> --reactome_path <reactome_path> --wikipathways_path <wikipathways_path> --yes -c -f -kp -rp -wp -y

pathme_viewer-manage-summarize command line option --connection <connection> -c pathme_viewer-web command line option --host <host> --port <port> --static <static> --template <template> --verbose -v pathme_viewer.manager (module) pathme_viewer.models (module) Pathway (class in pathme_viewer.models) pathway_id (pathme_viewer.models.Pathway attribute) pathway_tuple() (pathme_viewer.models.Pathway property) pybel_version (pathme_viewer.models.Pathway attribute)

Q

query_pathway_by_name() (pathme_viewer.manager.Manager method)

query_pathway_by_name_and_resource() (pathme_viewer.manager.Manager method)

R

resource_name (pathme_viewer.models.Pathway attribute)

V

version (pathme_viewer.models.Pathway attribute)