Metadata-Version: 2.1
Name: pyfastcore
Version: 0.0.6
Summary: A python-based implementation for the context-specific metabolic model extraction methods from Vlassis et al. 2014
Home-page: https://github.com/migp11/pyfastcore
Author: Miguel Ponce-de-Leon
Author-email: miguelponcedeleon@gmail.com
Maintainer: Miguel Ponce-de-Leon
Maintainer-email: miguelponcedeleon@gmail.com
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE

# pyfastcore

A python implementation of the context-specific model extraction method FastCore by Vlassis et al. (2014)

* Vlassis, N., Pacheco, M. P., & Sauter, T. (2014). PLoS Computational Biology, 10(1) [[Full Article]](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003424)

## INSTALATION

You can install pyfastcore using:
`python setup.py install`

of via pip:
`pip install pyfastcore`

## USAGE EXAMPLE
```
from cobra.test import create_test_model
from pyfastcore import Fastcore

# Loading a toy model of E. coli from cobra.test package
model = create_test_model('textbook')
# Define the list of core reactions
core_reactions = ['Biomass_Ecoli_core', 'ATPM']
# Setting the penalty of exchange fluxes to 0
penalties = {}
for r in model.exchanges:
    penalties[r.id] = 0

# Creating a fastcore solver instnace
fc_builder = Fastcore(model, core_reactions,
                      penalties=penalties,
                      default_penalty=10,
                      debug_mode=True)

# Rnunning fastcore
fc_builder.fast_core()

# checking the list of reaction in the consistent network found
consistent_subnetwork = fc_builder.consistent_subnetwork
print("Consistent subnetworksize set size", len(consistent_subnetwork))
print("Context specific core:")
print(consistent_subnetwork)

# creating a cobra model for the consistent network found
print(f"Building context-specific model for {model.id}")
cs_model = fc_builder.build_context_specific_model()

# Running and FBA using subnetwork model 
print("Running FBA on CS-model")
sol = cs_model.optimize()
print(cs_model.summary())

```


## Citation
If you use this package cite:
* Ponce-De-Leon, M. et al. (2015) Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach. PloS one, 10, e0143626.



