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harryscholes/kegg_api.sh

Created June 12, 2017 13:19
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Download all KEGG pathways and modules for an organism
Raw
kegg_api.sh
organism=spo
# Download S. pombe KEGG pathways
wget -O kegg_pathways.tsv http://rest.kegg.jp/list/pathway/${organism}
ids=$(cut -f1 kegg_pathways.tsv)
for id in $ids; do
wget -O ${id}.json http://togows.dbcls.jp/entry/pathway/${id}/genes.json
done
# Download S.pombe KEGG modules
wget -O kegg_modules.tsv http://rest.kegg.jp/list/module/${organism}
ids=$(cut -f1 kegg_modules.tsv)
for id in $ids; do
wget -O ${id}.json http://togows.dbcls.jp/entry/pathway/${id}/genes.json
done
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