#!/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")