KEGG pathway process, usage:
1. update local data table ($EXECUTINGPATH/KEGG_data/KEGG_organism.tsv):
$ Pathway Update
2. download organisms keg file (s):
$ Pathway Get hsa mmu ath
3. get keg file of an organism from local:
$ Pathway get hsa
Note: make sure you have download organisms' keg files and achieve to
$EXECUTINGPATH/KEGG_data/Pathway_keg.tar
4. find match species name or code in local data table:
$ Pathway match "Rhinopithecus roxellana"
$ Pathway match Rhinopithecus+roxellana
$ Pathway match rro
5. download pathway html:
$ Pathway HTML hsa00001.keg.gz ./hsa00001
Note: existing html files will not be overwritten
6. convert keg format to tsv (file or stdout):
$ Pathway tsv hsa00001.keg.gz hsa00001.keg.tsv
output tsv header: gene_id gene_information C_id C_name
KO_id KO_information EC_ids B_id B_name A_id A_name
7. download species keg, convert to tsv and download html files:
$ Pathway species Rhinopithecus+roxellana
Note: existing html files will be overwritten