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keggparser's Introduction

Parser for KEGG ftp files

4 files scripts to parse and create a node and edge flat file for import into R/neo4j.

mkdir a output dir mkdir misc

Parsing for CPD and KO details

  1. kegg.0100.ko_nodedetails.pl
  2. kegg.0200.cpd_nodedetails.pl
#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

Parsing each Pathway’s reactions

  1. kegg.0300.import.r
$ kegg.0300.import.r </path/to/keggFTP/root/folder> <misc> <# of threads>
# misc directory be where the ko_nodes cpd_nodes files be stored

Dependencies

R

Package version
dplyr 0.3.0.2
magrittr 1.5
XML 3.98-1.1
parallel

keggparser's People

Contributors

etheleon avatar

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