The ModelSEEDDatabase has been completely refactored and cleaned up but is now incompatible with PyFBA parsing scripts.

One of the latest versions that is currently compatible with PyFBA is c4ba1c6 (link). Checking out that version will work for now until parsing scripts are updated.

We need to implement a mechanism to correct role mapping from RAST to the biochemistry tables.

This file role_corrections.txt has a two column table with RAST role and Biochemistry role. When we are parsing assigned functions we just need to add these to the mapping.

Hi Rob,

I have successfully installed PyFBA using python2. However, I failed to update to python3 after following the instructions (recompile pyglpk). The output is "SyntaxError: Missing parentheses in call to 'print'.". Would you please share with me more details about how to update to python3 from python2?

Thanks,

Chen

We need to output the models in SBML and/or JSON format

Dear PyFBA developers,

Does PyFBA work with Python 3? When I try to install it from PyPI:

pip install pyfba

or clone from github and run tests

git clone https://github.com/linsalrob/PyFBA.git
cd PyFBA
python3 setup.py test

I get the same following error:

Traceback (most recent call last):
  File "setup.py", line 7, in <module>
    import PyFBA
  File "..../PyFBA/PyFBA/__init__.py", line 3, in <module>
    import fba
ImportError: No module named 'fba'

Thanks,
Anna

I recently installed pyfba v 2.62 (using python3) and I was running through the "How to create and run a gap-filled FBA from PATRIC" iPython notebook. I kept receiving an warning messages on the runfba step (In [14] in the notebook) about "set" and "modeldata" objects, and the command didn't seem to complete properly.

After digging into the source code, it looks like the create_stoichiometric_matrix.py code may have an error on line 52 where it calls "if not set.get_compound_by_name(c.name):". I changed this to "if not modeldata.get_compound_by_name(c.name):" and then changed code for running the fba to include lines for creating a modeldata object from compounds and reactions and then using that object in the run_fba command (see below).

#status, value, growth = PyFBA.fba.run_fba(compounds, reactions, reactions_to_run, media, biomass_equation)
modeldata = PyFBA.model_seed.ModelData(compounds=compounds, reactions=reactions)
modeldata.rebuild_indices()
status, value, growth = PyFBA.fba.run_fba(modeldata, reactions_to_run, media, biomass_equation)

Hi, I am trying to run the model_seed.py and it is depended to ComplexRoles.tsv and TemplateReactions.tsv files. Yet I could not figure out how I will dump/extract these files. I have tried to run the DumpSOLRTables_Master.pl which is in ModelSEEDDatabase via Cygwin64 for this purpose, yet I am getting some errors unfortunately. I have mentioned about these errors in the link below:

https://stackoverflow.com/questions/65801561/perl-error-global-symbol-requires-explicit-package-name

How can I obtain these 2 files exactly, I wonder? Or what are the templates of these files, so maybe I can create these files manually by using other existed files? If you can help me, I would be really glad. Thank you in advance.
Sincerely,

I have followed the instructions in creating the ModelSEEDDatabase variable as shown below;

thomas@Kiwi:~/PyFBA$ echo $ModelSEEDDatabase
/home/thomas/PyFBA/ModelSEEDDatabase

However when I test the setup.py code the following occurs;

thomas@Kiwi:~/PyFBA$ python setup.py test
Traceback (most recent call last):
File "setup.py", line 7, in
import PyFBA
File "/home/thomas/PyFBA/PyFBA/init.py", line 5, in
import PyFBA.gapfill
File "/home/thomas/PyFBA/PyFBA/gapfill/init.py", line 13, in
from .ecnumbers import suggest_reactions_using_ec
File "/home/thomas/PyFBA/PyFBA/gapfill/ecnumbers.py", line 5, in
MODELSEED_DIR = os.environ['ModelSEEDDatabase']
File "/usr/lib/python2.7/UserDict.py", line 23, in getitem
raise KeyError(key)
KeyError: 'ModelSEEDDatabase'

Any idea how to solve this?