model-polisher

API for the Model Polisher.

• API version: 2.1
• Package version: 2.1.0

Getting Started

import libsbml
import model_polisher as mp

model_file = "path/to/iAF1260 .xml"
sbml = libsbml.readSBMLFromFile(model_file)

config = {"annotation": {"bigg": {"annotate-with-bigg": "false"},
                         "annotatedb": {"annotate-with-adb": "false"}}}

# you can pass a file
result = mp.polish_model_file(config, model_file)

# or you can pass a libsbml.SBMLDocument object
result2 = mp.polish_model_document(config, sbml)

# result is a dictionary with five keys:
# result["run_id"] # server-side run id for troubleshooting
# result["diff"] # datastructure that attempts to show all the changes that were performed by the polisher
# result["pre_validation"] # validation before the polisher was used
# result["pre_validation"] # validation after the polisher was used
# result["polished_document"] # libsbml.SBMLDocument object

You can find the config options here.

Requirements.

Python 2.7 and 3.4+

Installation & Usage

pip install

Right now, the package is only hosted on GitHub. You can install it like this:

pip install git+https://github.com/draeger-lab/MPClient.git

Setuptools

Install via Setuptools.

python setup.py install --user