Add COBRApy sample code

.gitignore

+.idea/*
+!.idea/runConfigurations/
+venv/

install.sh

+pip install git+https://github.com/shjchan/cobrapy.git@implement_find_act_rxns
+pip install lxml
+pip install scipy
\ No newline at end of file

run.py

+#!/usr/bin/env python3
+# coding: utf-8
+
+from argparse import ArgumentParser
+from os import path, mkdir
+from timeit import default_timer as timer
+
+from cobra.flux_analysis import flux_variability_analysis, add_loopless
+from cobra.io import read_sbml_model
+
+parser = ArgumentParser(description="FVA Solver")
+parser.add_argument("--model", help="SBML file with the model")
+parser.add_argument("--method", help="Loop removal method", default="fastSNP")
+args = parser.parse_args()
+
+workdir = f"instances/{args.model}/"
+outdir = path.join(workdir, "output")
+if not path.exists(outdir):
+    mkdir(outdir)
+file = path.join(workdir, f"{args.model}.xml")
+
+model = read_sbml_model(file)
+model.solver = "cplex"
+# model.objective = "FRD7"
+
+print(f"Number of reactions: {len(model.reactions)}")
+print(f"Number of metabolites: {len(model.metabolites)}")
+
+time = timer()
+add_loopless(model, zero_cutoff=1E-6, method=args.method)
+fba = model.optimize(raise_error=True)
+time = timer() - time
+print(f"Time: {time}")
+print(f"FBA objective: {fba.objective_value}")
+fba.fluxes.to_csv(path.join(outdir, f"cobrapy-fba-{args.method}.tsv"), sep='\t', header=True)
+
+for optimum in [0.0, 1.0]:
+    fva = flux_variability_analysis(model, model.reactions, loopless=False, fraction_of_optimum=optimum)
+    outfile = path.join(outdir, f"cobrapy-fva-{args.method}-opt{optimum}.tsv")
+    fva.to_csv(outfile, sep='\t', encoding="utf-8", float_format="%.10f")