Command Line Interface¶
PathMe-Viewer commands.
pathme_viewer¶
PathMe
pathme_viewer [OPTIONS] COMMAND [ARGS]...
manage¶
Manage the database.
pathme_viewer manage [OPTIONS] COMMAND [ARGS]...
Options
-
-c
,
--connection
<connection>
¶ Cache connection. Defaults to sqlite:////home/docs/.bio2bel/bio2bel.db
drop¶
Delete all database entries
pathme_viewer manage drop [OPTIONS]
Options
-
-v
,
--debug
¶
Turn on debugging.
-
-y
,
--yes
¶
-
-c
,
--connection
<connection>
¶ Cache connection. Defaults to sqlite:////home/docs/.bio2bel/bio2bel.db
export-to-tsv¶
Export pathways to tsv
pathme_viewer manage export-to-tsv [OPTIONS]
Options
-
-c
,
--connection
<connection>
¶ Defaults to sqlite:////home/docs/.bio2bel/bio2bel.db
-
-a
,
--all
¶
load¶
Load Pathways
pathme_viewer manage load [OPTIONS]
Options
-
-c
,
--connection
<connection>
¶ Cache connection. Defaults to sqlite:////home/docs/.bio2bel/bio2bel.db
-
-kp
,
--kegg_path
<kegg_path>
¶ KEGG data folder. Defaults to /home/docs/.pathme/kegg
-
-rp
,
--reactome_path
<reactome_path>
¶ Reactome data folder. Defaults to /home/docs/.pathme/reactome
-
-wp
,
--wikipathways_path
<wikipathways_path>
¶ WikiPathways data folder. Defaults to /home/docs/.pathme/wikipathways
-
-f
,
--flatten
<flatten>
¶ Flat complexes/composites. Defaults to False
-
-y
,
--yes
¶
Skip confirmation