Saving an epistasis model

All epistasis models/simulators store epistatic coefficients in Pandas Series/DataFrames, so the coefficients can be written to various file formats. This page lists a few.

Pickle

The recommended way to save an epistasis model to be used again is by pickling the model(See Python’s pickle library).

# Import pickle module
import pickle
from epistasis.models import EpistasisLinearRegression

# Simple model object
model = EpistasisLinearRegression(model=1)

# Save to disk to open later.
with open('model.pickle', 'wb') as f:
    pickle.dump(f, model)

To load the saved model,

# Import pickle module
import pickle

# Read from file.
with open('model.pickle', 'rb') as f:
    model = pickle.load(f)

Warning

Pickled models will only work with the same version of the epistasis package that created it. If you save a model and upgrade the library, you likely won’t be able to use the model anymore.

Excel Spreadsheet

Epistatic coefficients can be written to an excel file using the to_excel method

model.to_excel('data.xlsx')

	sites	values
0	[0]	0.501191
1	[1]	-0.600019
2	[2]	0.064983
3	[3]	0.609166
4	[4]	0.242095
5	[1, 2]	0.286914
6	[1, 3]	-0.264455
7	[1, 4]	-0.464212
8	[2, 3]	0.638260
9	[2, 4]	0.235989
10	[3, 4]	0.717954
11	[1, 2, 3]	-0.473122
12	[1, 2, 4]	-0.041919
13	[1, 3, 4]	-0.309124
14	[2, 3, 4]	0.606674
15	[1, 2, 3, 4]	-0.268982

CSV File

Epistatic coefficients can be written to a csv file using the to_csv method

model.epistasis.to_csv('epistasis.csv')

,sites,values
0,[0],0.5011910655025966
1,[1],-0.6000186681513706
2,[2],0.06498276930060931
3,[3],0.6091656756721153
4,[4],0.24209508436556937
5,"[1, 2]",0.2869142038187855
6,"[1, 3]",-0.26445514455225094
7,"[1, 4]",-0.4642116520437949
8,"[2, 3]",0.638260262428922
9,"[2, 4]",0.23598864236123118
10,"[3, 4]",0.7179538630349485
11,"[1, 2, 3]",-0.47312160287366267
12,"[1, 2, 4]",-0.04191888437610514
13,"[1, 3, 4]",-0.30912353449573415
14,"[2, 3, 4]",0.6066739725656609
15,"[1, 2, 3, 4]",-0.2689818206753505