pombase-gocam-tool

PomBase tool for processing GO-CAM models.

Compilation

cargo build --release

Sub-commands

• all-genes
• check-allowed-relations
• connected-genes
• cytoscape
• cytoscape-model-connections
• cytoscape-model-connections-with-rel-nodes
• cytoscape-simple
• cytoscape-simple-merged
• detached-chemicals
• detached-genes
• find-holes
• find-missing-evidence
• find-obsolete-terms
• genes-enabling-activities
• gocam-py-parse-test
• graph-viz-dot
• joining-chemicals
• make-chado-data
• overlapping-nodes
• per-model-stats
• print-edges
• print-individuals
• print-nodes
• print-tuples
• print-unconnected-individuals
• serialize
• total-stats - Find MF, BP or CC with missing evidence
• find-missing - Find missing BP or CC
• write-annotation

Examples commands

curl https://raw.githubusercontent.com/pombase/pombase-gocam/refs/heads/main/tests/data/gomodel%3A66187e4700001744.json > gomodel:66187e4700001744.json
pombase-gocam-tool find-holes gomodel:66187e4700001744.json | less -S
pombase-gocam-tool stats gomodel:66187e4700001744.json | less -S
pombase-gocam-tool print-nodes gomodel:66187e4700001744.json | less -S