1. # download pathway KO genome
  2. wget -c http://rest.kegg.jp/list/pathway
  3. wget -c http://rest.kegg.jp/list/ko
  4. wget -c http://rest.kegg.jp/list/genome
  6. # KO list
  7. mkdir KO_files
  8. cut -f 1 ko | sed 's/ko://' | while read id; do wget -c http://rest.kegg.jp/link/genes/$id -O KO_files/$id; done
  9. cat KO_files/K* | sed 's/ko://' > ko_genes.txt
  11. # gene list
  12. mkdir gene_files
  13. cut -f 2 genome | cut -f 1 -d "," | while read id; do wget -c http://rest.kegg.jp/list/$id -O gene_files/$id; done
  14. cat gene_files/* | cut -f 1 > all_genes.list
  16. # gene fasta
  17. mkdir gene_fasta
  18. cat all_genes.list | while read id; do wget -c http://rest.kegg.jp/get/$id/aaseq -O gene_fasta/$id; done
  19. cat gene_fasta/* > kegg_genes.fasta

Reference

  1. download KEGG database