fix_bounds.py

from lxml.etree import parse, Element, SubElement, \
    ElementTree, register_namespace, ParseError, XPath, \
    XMLParser

from cobra.io.sbml3 import namespaces, strnum, ns


def add_in_flux_bounds(filename, outfile=None, min_value=-1000,
                       max_value=1000):
    if outfile is None or outfile == "":
        outfile = "fixed_" + filename
    doc = parse(filename, XMLParser(remove_blank_text=True))
    xml_model = doc.find("sbml:model", namespaces=namespaces)
    parameter_list = xml_model.find("sbml:listOfParameters",
                                    namespaces=namespaces)
    if parameter_list is None:
        parameter_list = parameter_list = SubElement(xml_model,
                                                     "listOfParameters")
    param_attr = {"constant": "true"}
    SubElement(parameter_list, "parameter", value=strnum(min_value),
               id="cobra_default_lb", sboTerm="SBO:0000626", **param_attr)
    SubElement(parameter_list, "parameter", value=strnum(max_value),
               id="cobra_default_ub", sboTerm="SBO:0000626", **param_attr)
    SubElement(parameter_list, "parameter", value="0",
               id="cobra_0_bound", sboTerm="SBO:0000626", **param_attr)

    for sbml_reaction in xml_model.iterfind(
            "sbml:listOfReactions/sbml:reaction", namespaces=namespaces):
        sbml_reaction.set(ns("fbc:upperFluxBound"), "cobra_default_ub")
        if sbml_reaction.get("reversible") == "true":
            sbml_reaction.set(ns("fbc:lowerFluxBound"), "cobra_0_bound")
        else:
            sbml_reaction.set(ns("fbc:lowerFluxBound"), "cobra_default_lb")
    doc.write(outfile, pretty_print=True, encoding="UTF-8",
              xml_declaration=True)

if __name__ == "__main__":
    import argparse
    parser = argparse.ArgumentParser(description='Add flux bounds to a model')
    parser.add_argument("filename")
    parser.add_argument("-o", "--outfile")
    parser.add_argument("--min", default=-1000)
    parser.add_argument("--max", default=1000)

    args = parser.parse_args()
    add_in_flux_bounds(args.filename, args.outfile, args.min, args.max)