RbioRXN (version 1.3.1)

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)