gene - reaction - metabolite associations

associations.py

from framed import load_cbmodel
import pandas as pd

model = load_cbmodel("iML1515.xml.gz", flavor="bigg")

gene2met = [(g_id, r_id, m_id) for r_id, rxn in model.reactions.items()
                               for g_id in rxn.get_associated_genes()
                               for m_id in rxn.stoichiometry]

df = pd.DataFrame(gene2met, columns=["metabolites",  "reactions", "genes"])

df.to_csv("associations.tsv", sep="\t", index=False)