3. Preparing Single Gene Target and Double Gene Combinations

import os
from scarcc.preparation.find_directory import find_directory
data_directory = find_directory('Data', os.path.abspath(''))

3.1. Read double gene from first column of GeneCombos file

from scarcc.preparation.target_gene.gene_combination_handler import (get_DG_list, get_SG_list, generate_all_combinations)
DG_list = get_DG_list(os.path.join(data_directory, 'GeneCombos.csv'), n_combos=None)
DG_list[:5]

[('dadX', 'aroA'),
 ('dadX', 'eno'),
 ('dadX', 'pheA'),
 ('dadX', 'acnB'),
 ('aroA', 'dapF')]

3.2. Get all single genes from double gene list

SG_list = get_SG_list(DG_list)
SG_list[:10]

['murA', 'pyrD', 'purT', 'dapD', 'folP', 'ackA', 'pheA', 'dapA', 'eno', 'tktA']

potential_DG = generate_all_combinations(SG_list)
potential_DG[:5]

There are 465 potential gene combinations

[('murA', 'pyrD'),
 ('murA', 'purT'),
 ('murA', 'dapD'),
 ('murA', 'folP'),
 ('murA', 'ackA')]

Since quantity of total gene combinations = \(C^n_2\), N = number of target genes

Initial screening in FBA could be desired to observe drug combination effect for single species using COBRA