Mercurial > repos > laurenmarazzi > netisce_test
comparison tools/myTools/bin/sfa/data/cho_2016/__init__.py @ 1:7e5c71b2e71f draft default tip
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author | laurenmarazzi |
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date | Wed, 22 Dec 2021 16:00:34 +0000 |
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0:f24d4892aaed | 1:7e5c71b2e71f |
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1 # -*- coding: utf-8 -*- | |
2 | |
3 """ | |
4 [Reference] | |
5 Cho et al. | |
6 Attractor landscape analysis of | |
7 colorectal tumorigenesis and its reversion. | |
8 BMC Systems Biology (2016) 10:96. | |
9 """ | |
10 | |
11 import os | |
12 | |
13 import pandas as pd | |
14 | |
15 import sfa | |
16 import sfa.base | |
17 | |
18 | |
19 def create_data(): | |
20 return ChoData() | |
21 | |
22 | |
23 class ChoData(sfa.base.Data): | |
24 | |
25 def __init__(self): | |
26 | |
27 self._abbr = "CHO_2015" | |
28 self._name = "Cho et al. BMC Systems Biology (2016) 10:96" | |
29 | |
30 inputs = {} | |
31 inputs['ECM'] = 1.0 | |
32 inputs['Tgf-b'] = 1.0 | |
33 inputs['IL1-TNF'] = 1.0 | |
34 inputs['EGF'] = 1.0 | |
35 inputs['alpha_i_lig'] = 1.0 | |
36 inputs['alpha_12_13_lig'] = 1.0 | |
37 inputs['alpha_s_lig'] = 1.0 | |
38 inputs['alpha_q_lig'] = 1.0 | |
39 inputs['Stress'] = 1.0 | |
40 inputs['WNT'] = 1.0 | |
41 inputs['Fas'] = 1.0 | |
42 inputs['ExtPump'] = 1.0 | |
43 inputs['DNA_damage'] = 1.0 | |
44 | |
45 dpath = os.path.dirname(__file__) | |
46 fpath_network = os.path.join(dpath, 'network_all_pos.sif') | |
47 A, n2i, dg = sfa.read_sif(fpath_network, as_nx=True) | |
48 self._A = A | |
49 self._n2i = n2i | |
50 self._i2n = {idx: name for name, idx in n2i.items()} | |
51 self._dg = dg | |
52 self._inputs = inputs | |
53 | |
54 | |
55 # end of def __init__ | |
56 # end of def class | |
57 |