Adding PyFBA.model package to list.
However, this breaks compatibility with Python 2 because of the "errors" keyword in open.
The main changes include relative imports, a new class in the tests/ package to allow deep assertions, and using this type of construct with the open command to ignore unicode errors in ModelSeed:
with open(ssfile, 'r', errors='replace') as sin:
- PyFBA/filters/roles_and_complexes.py
- PyFBA/gapfill/ecnumbers.py
- PyFBA/gapfill/reaction_minimization.py
Model object contains functionality to make common processes easier to facilitate.
- Generate model from RAST annotations
- Save model to hard disk location
- Load model from hard disk location
- Run FBA
- Run FBA and obtain flux values
- Run FBA and obtain flux values according to SEED subsystems
- Run gap-fill
- Remember which reactions were gap-filled reactions and which media
- Find a metabolite.ipynb
- PATRIC to FBA.ipynb
- Gap-fill_a_model.ipynb
- Saving_and_loading_a_model.ipynb
Please cite us if you use PyFBA
Example code showing:
importing an SBML file and running FBA
- iPythonNotebooks/Using_an_SBML_model.ipynb
how to build your model from functional roles and how to gap-fill that model on a media
- iPythonNotebook/From_functional_roles_to_gap-filling.ipynb
Removed PyFBA/gapfill/minimize_additional_reactions.py and created reaction_minimization.py
- example_code/gapfill_from_reactions_multiple_conditions.py
It is superflous, that is what versioning is for.
Several changes to files:
Updated the subsystem functions and changed the name to a generic name. The date is handled by versioning!
- PyFBA/Biochemistry/SEED/Subsystems/SS_functions.txt
- PyFBA/Biochemistry/SEED/Subsystems/SS_functions_Oct_2015.txt
- PyFBA/init.py
- PyFBA/fba/init.py
- PyFBA/fba/fluxes.py
Fixed an issue where we were over-incorporating reactions based on things in the media
- PyFBA/fba/bounds.py
- PyFBA/parse/model_seed.py
- PyFBA/fba/run_fba.py
- PyFBA/gapfill/roles.py
- PyFBA/parse/read_media.py
We only test the right half of the reactions if the left half do not grow, and once we have <10 reactions to search through we just iterate and knock out each reaction sequentially. It is faster than the shuffle approach.
- PyFBA/gapfill/minimize_additional_reactions.py
SEED has a notion of multifunctional roles, and we added splitting those functions into roles
- PyFBA/gapfill/subsystem.py
Testing each of the individual reactions in a model
- PyFBA/gapgeneration/test_reactions.py
- example_code/test_individual_reactions.py
This order makes more logical sense!
- example_code/gapfill_from_reactions.py
With all these changes, the tests were not right
- PyFBA/tests/reaction_list.txt
- PyFBA/tests/test_fba.py
- PyFBA/tests/test_suggestions.py
Refactored separating roles to functions. SEED has a concept of multifunctional roles and this separates out our roles before we search for them.
- Removed installation dependencies from setup.py because they break installation! You need to install the dependencies manually
- Refactored the code to remove the os.environ dependencies
- Initial release