Friday, June 08, 2018

Download all KEGG pathway KGML files for SPIA analysis

Most people know KEGG pathway, but not everyone knows that it costs at least $2000 to subscribe its database. If you want to save the cost a bit, you can manually download the KEGG pathway KGML files and install in SPIA. Here I have a workaround to download all KEGG pathway files using their REST API.
## Claim: this is my personal trick. I recommend people to subscribe their KEGG FTP download to support the authors.

# change folder to the folder where your SPIA installed
cd /Library/Frameworks/R.framework/Versions/3.4/Resources/library/SPIA
# download all XML files for all human pathway
curl -s http://rest.kegg.jp/list/pathway/hsa | awk '{split($1,a,":"); print "curl -s http://rest.kegg.jp/get/"a[2]"/kgml -o extdata/keggxml/hsa/"a[2]".xml"}' | bash

# then switch to R console
setwd("/Library/Frameworks/R.framework/Versions/3.4/Resources/library/SPIA")
library(SPIA)
makeSPIAdata(kgml.path=system.file("extdata/keggxml/hsa",package="SPIA"),organism="hsa",out.path="./extdata")

Done!

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