parse.metacyc.reaction: Parse MetaCyc reaction data (reactions.dat in attribute-value...
In RbioRXN: Process Rhea, KEGG, MetaCyc, Unipathway Biochemical Reaction Data

Description Usage Arguments Value Author(s) Examples

Parse MetaCyc reactions.dat file in attribute-value format. The output includes reaction ID, enzyme, EC number, pathway and equation

1	parse.metacyc.reaction(datPath)

datPath

Path to reactions.dat from MetaCyc (BioCyc or EcoCyc data also applicable)

data.frame() object where data fields include

`UNIQUE.ID`
`TYPES`
`ATOM.MAPPINGS`
`CITATIONS`
`COMMENT`
`CREDITS`
`DBLINKS`
`IN.PATHWAY`
`LEFT`
`PHYSIOLOGICALLY.RELEVANT.`
`REACTION.DIRECTION`
`RIGHT`
`CANNOT.BALANCE.`
`ENZYMATIC.REACTION`
`ORPHAN.`
`SPONTANEOUS.`
`RXN.LOCATIONS`
`EC.NUMBER`
`COMMON.NAME`
`TEMPLATE.FILE`
`SYNONYMS`
`SYSTEMATIC.NAME`
`DELTAG0`
`COMMENT.INTERNAL`
`ENZYMES.NOT.USED`
`REACTION.LIST`
`MEMBER.SORT.FN`
`STD.REDUCTION.POTENTIAL`
`PREDECESSORS`
`PRIMARIES`
`SIGNAL`
`equation`
`LIGAND.RXN`
`PLANTCYC`
`METACYC`
`RHEA`
`UNIPROT`
`PIR`
`LIGAND`
`BRENDA`
`superNode`

Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol Choi

url = "http://bioinformatics.ai.sri.com/ptools/flatfile-samples/reactions.dat"
tmpdest = tempfile(pattern = "reactions")
download.file(url, destfile=tmpdest)

direction = "LEFT-TO-RIGHT" # sample data is old, so don't mind this code.
sample.reactions = parse.metacyc.reaction(datPath=tmpdest)
print(sample.reactions)