Installation¶

Use pip3 to install metquest from PyPI:

Via Python Package¶

pip3 install metquest

Direct installation¶

Install Python 3.4 or higher
Clone this repository to your computer using git or download the repository and decompress it.
Navigate to the folder where metquest is downloaded and type

python setup.py install

(Elevated sudo rights may be required depending on the platform. Replace python with python3 when multiple python distributions are found.)

Required python packages¶

cobra >= 0.11.3
numpy >= 1.14.3
scipy
python-libsbml
networkx >= 2.1

Input¶

Folder whose structure is as shown:

mainfolder/
|-Example1/
|   |-- SBML model(s) of metabolic networks # XML files of the metabolic networks(COBRA-compatible)
|   |-- seed_mets.txt       # Text file containing the seed metabolites separated by a newline
|   │-- source_mets.txt     # Text file containing the source metabolites separated by a newline
|   |-- target_mets.txt     # Text file containing the target metabolites separated by a newline
|   |-- cutoff.txt          # Text file containing the size cut-offs separated by a newline
|-Example2/
|   ...

Kindly ensure that the SBML model has the field <model id> and the metabolites are prefixed with the model identifiers, for instance, if the model identifier is ‘ecoli_core_model’, and the seed metabolite is ‘fum_c’, the input text file should contain ecoli_core_model fum_c

Running MetQuest¶

From command line¶

MetQuest can be directly run from the terminal as

metquest.sh <path containing the input folder>

Navigate to the folder where metquest is installed and type

python execute_metquest.py <path containing the input folder>

(Replace python with python3 when multiple python distributions are found.)

From python console¶

>>> import metquest
>>> metquest.execute_all_codes()

When prompted, enter the path containing the folder with all the data files

Running examples¶

In the python console, type the following

>>> import metquest
>>> metquest.example.run_this_example()

This will run the example files.