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