Python 3.7+, DSGRN+dependencies, networkx
From the command line, do
. install.shor
source install.sh
inside of the top-level folder dsgrn_utilities. Tests will be run as part of the installation process. One set of tests is dependent on having the DSGRN git repository in the same folder as the dsgrn_utilities repository, and will fail if that is not true.
Every function has a doc string. The test scripts in the tests folder provide some examples on how to use the modules. Limited cases addressed below.
#Commands
This repository is set up as a library, not as a collection of callable scripts. The user is expected to write their own scripts.
import DSGRN
import dsgrn_utilities.select_boolean_params as sbp
def get_MBFs(networkfile,path2DSGRN):
network = DSGRN.Network(networkfile)
MBFs = sbp.subset_boolean_parameters(network,path2DSGRN)
return MBFs
The variable MBFs is a list of DSGRN.Parameter objects. From these, you can work in pure python to find Morse graphs. In some cases, it will be useful to have the parameter indices in order to use a DSGRN database or to find the MBF neighbors.
To get the parameter indices, do
import DSGRN
def get_MBF_indices(network,MBFs):
param_graph = DSGRN.ParameterGraph(network)
MBF_indices = [param_graph.index(param) for param in MBFs]
return MBF_indices
To find the MBF indices and the DSGRN neighbors of the MBFs at the same time, do
import DSGRN
import dsgrn_utilities.get_parameter_neighbors as pn
def get_MBF_neighbors(networkfile, path2DSGRN):
network = DSGRN.Network(networkfile)
MBF_indices, neighbors = pn.get_Boolean_parameter_neighbors(network,path2DSGRN)
return MBF_indices, neighborsThe MBF_indices do not include duplicates; i.e., those neighbors of MBFs that only exhibit a threshold permutation and therefore are exactly the same MBF. The neighbor list also includes no MBFs, regardless of threshold perturbation. However, the neighbors list includes all neighbors of MBFs across all threshold permutations.
To come.
Actively maintained. Contact me via GitHub with any issues or feature requests.