4 files scripts to parse and create a node and edge flat file for import into R/neo4j.
mkdir a output dir
mkdir misc
#Parse KOs
$ kegg.0100.ko_nodedetails.pl ~/KEGG/KEGG_SEPT_2014/genes/ko/ko > misc/ko_nodedetails
#Parse CPDs
$ kegg.0200.cpd_nodedetails.pl ~/KEGG/KEGG_SEPT_2014/ligand/compound/compound ~/KEGG/KEGG_SEPT_2014/ligand/glycan/glycan > misc/cpd_nodedetails
$ kegg.0300.import.r </path/to/keggFTP/root/folder> <misc> <# of threads>
# misc directory be where the ko_nodes cpd_nodes files be stored
Package | version |
---|---|
dplyr | 0.3.0.2 |
magrittr | 1.5 |
XML | 3.98-1.1 |
parallel |