示例#1
0
def visualize_model(sbml, vis_r_ids, id2mask, id2color, title, info, invisible_layers, layer2mask, res_dir, tab2html):
    combined_sbml = os.path.join(res_dir, "Combined_model.xml")
    r_ids2sbml(vis_r_ids, sbml, combined_sbml, "combined")
    doc = libsbml.SBMLReader().readSBML(combined_sbml)
    model = doc.getModel()
    id2mask = get_full_id2mask(id2mask, model)
    process_sbml(
        combined_sbml,
        verbose=True,
        web_page_prefix="visualization",
        generalize=False,
        id2mask=id2mask,
        layer2mask=layer2mask,
        tab2html=tab2html,
        title=title,
        id2color=id2color,
        tabs=None,
        info=info,
        invisible_layers=invisible_layers,
    )
示例#2
0
# !/usr/bin/env python
# encoding: utf-8

from sbml_vis.mimoza_pipeline import process_sbml

__author__ = 'anna'

if __name__ == "__main__":

    # parameter parsing #
    import argparse

    parser = argparse.ArgumentParser(
        description="Generalizes and visualizes an SBML model.")
    parser.add_argument('--model',
                        required=True,
                        type=str,
                        help="input model in SBML format")
    parser.add_argument('--verbose',
                        action="store_true",
                        help="print logging information")
    params = parser.parse_args()

    process_sbml(params.model,
                 params.verbose,
                 ub_ch_ids=None,
                 web_page_prefix=None,
                 generalize=True,
                 log_file=None)
示例#3
0
# !/usr/bin/env python
# encoding: utf-8

from sbml_vis.mimoza_pipeline import process_sbml

__author__ = 'anna'

if __name__ == "__main__":

    # parameter parsing #
    import argparse

    parser = argparse.ArgumentParser(description="Generalizes and visualizes an SBML model.")
    parser.add_argument('--model', required=True, type=str, help="input model in SBML format")
    parser.add_argument('--verbose', action="store_true", help="print logging information")
    params = parser.parse_args()

    process_sbml(params.model, params.verbose, ub_ch_ids=None, web_page_prefix=None, generalize=True, log_file=None)