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,
)
# !/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)
# !/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)