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