RbioRXN (version 1.5.1)

parse.metacyc.reaction: Parse MetaCyc reaction data (reactions.dat in attribute-value format)

Description

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

Usage

parse.metacyc.reaction(datPath)

Arguments

datPath

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

Value

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

Examples

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)