List all KEGG reaction IDs for organism with Orange.bio.kegg module Python

Question

[jolespin]

I'm following the documentation on http://pythonhosted.org/Orange-Bioinformatics/reference/kegg.html

I want to get an iterable for all the KEGG reaction IDs for a particular organism.

I chose my organism by:

#!/usr/bin/python
import Orange 
from Orange.bio.kegg import *

#Organism
genome = KEGGGenome()
genome_ids = genome.keys()
org_query = 'Escherichia coli K-12 MG1655'
org_id = None
for id in genome_ids:
    species = genome[id].definition
    if species == org_query:
        org_id = id
        break
organism = Organism(org_id) #T00007
org_code = organism.org_code #eco

I was able to get all the genes by:

#Genes
genes = organism.genes
gene_ids = genes.keys()
for id in gene_ids: 
    print id, genes[id].definition​

I got all of the pathway ids by:

#Pathways 1
pathways = organism.pathways()
for id in pathways:
    print id​

To get the pathway ids and names, I had to:

#Pathways 2
for path in Orange.bio.kegg.pathways(org_id):
    print path.entry_id, path.definition​

I'm trying to get the reaction ids and reaction names but I can't seem to get it to work. I started by creating the following object but I couldn't seem to get anything out of it.

#Reactions
reactions = Orange.bio.kegg.databases.Reaction()

Answer 1

[jolespin]

#Reactions Example for Glycolysis
cpd_db = Orange.bio.kegg.databases.Compound()
path_db = Orange.bio.kegg.databases.Pathway()
gly = 'eco00010'
for cpd_id in path_db.get_entry(gly).compound:
    print cpd_db.get_entry(cpd_id).reaction.replace('\n','').split(' ')