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Commit 8e3c600

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DeshanPereraDeshanPerera
committed
update default param
1 parent 8943ba0 commit 8e3c600

4 files changed

Lines changed: 213 additions & 5 deletions

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‎default_Parameter_Files_Apollo/CATE_app‎

9.06 MB
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‎default_Parameter_Files_Apollo/convert_Files/Mutation_Sites_to_JSON.csv‎

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Hotspot_index,Position_start,Position_stop,Clock_model,Poisson_mean,Negative_Binomial_Sucess,Negative_Binomial_Probability,Fixed_probability,AA,AT,AG,AC,TA,TT,TG,TC,GA,GT,GG,GC,CA,CT,CG,CC
2+
1,38,38,Poisson,0.33333,NA,NA,NA,0.9,0,0.1,0,0.85,0,0.15,0,0.55,0,0.45,0,0.85,0,0.15,0
3+
2,47,47,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05
4+
3,49,49,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
5+
4,51,51,Poisson,0.33333,NA,NA,NA,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0
6+
5,53,53,Poisson,0.33333,NA,NA,NA,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0
7+
6,57,57,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
8+
7,60,60,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
9+
8,61,61,Poisson,0.33333,NA,NA,NA,0.2,0,0.8,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
10+
9,69,69,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.9,0,0.1,0,0.95,0,0.05,0
11+
10,77,77,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.9,0,0.1
12+
11,85,85,Poisson,0.33333,NA,NA,NA,0.1,0,0.9,0,0.1,0,0.9,0,0.1,0,0.9,0,0.1,0,0.9,0
13+
12,86,86,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
14+
13,87,87,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
15+
14,89,89,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
16+
15,90,90,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
17+
16,100,100,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05
18+
17,101,101,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.9,0,0.1
19+
18,105,105,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.8,0,0.2,0,0.95,0,0.05,0
20+
19,106,106,Poisson,0.33333,NA,NA,NA,0.1,0,0.9,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
21+
20,107,107,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.8,0,0.2,0,0.95,0,0.05,0
22+
21,108,108,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
23+
22,110,110,Poisson,0.33333,NA,NA,NA,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0
24+
23,115,115,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
25+
24,118,118,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
26+
25,121,121,Poisson,0.33333,NA,NA,NA,0.33,0.33,0,0.34,0.33,0.33,0,0.34,0.33,0.33,0,0.34,0.33,0.33,0,0.34
27+
26,126,126,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
28+
27,130,130,Poisson,0.33333,NA,NA,NA,0.1,0,0.9,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
29+
28,135,135,Poisson,0.33333,NA,NA,NA,0.5,0,0.5,0,0.5,0,0.5,0,0.5,0,0.5,0,0.5,0,0.5,0
30+
29,136,136,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
31+
30,137,137,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
32+
31,139,139,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
33+
32,146,146,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
34+
33,149,149,Poisson,0.33333,NA,NA,NA,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0
35+
34,150,150,Poisson,0.33333,NA,NA,NA,0.02,0.96,0.02,0,0.02,0.96,0.02,0,0.02,0.96,0.02,0,0.02,0.96,0.02,0
36+
35,153,153,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
37+
36,159,159,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
38+
37,168,168,Poisson,0.33333,NA,NA,NA,0,0.1,0,0.9,0,0.2,0,0.8,0,0.1,0,0.9,0,0.1,0,0.9
39+
38,174,174,Poisson,0.33333,NA,NA,NA,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0
40+
39,178,178,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
41+
40,181,181,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.9,0,0.1
42+
41,186,186,Poisson,0.33333,NA,NA,NA,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95
43+
42,188,188,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05
44+
43,192,192,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
45+
44,193,193,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
46+
45,194,194,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
47+
46,195,195,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
48+
47,199,199,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
49+
48,202,202,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.8,0,0.2,0,0.95,0,0.05,0
50+
49,204,204,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.5,0,0.5
51+
50,209,209,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,0.25,0,0.75,0,1,0,0,0
52+
51,210,210,Poisson,0.33333,NA,NA,NA,0.8,0,0.2,0,0.8,0,0.2,0,0.75,0,0.25,0,0.8,0,0.2,0
53+
52,219,219,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.8,0,0.2,0,0.95,0,0.05,0
54+
53,220,220,Poisson,0.33333,NA,NA,NA,0,0.9,0.1,0,0,0.9,0.1,0,0,0.9,0.1,0,0,0.9,0.1,0
55+
54,227,227,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.8,0,0.2,0,0.95,0,0.05,0
56+
55,231,231,Poisson,0.33333,NA,NA,NA,0,0.03,0,0.97,0,0.03,0,0.97,0,0.03,0,0.97,0,0.03,0,0.97
57+
56,235,235,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
58+
57,237,237,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
59+
58,239,239,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.8,0,0.2
60+
59,245,245,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
61+
60,246,246,Poisson,0.33333,NA,NA,NA,0.2,0,0.8,0,0.2,0,0.8,0,0.2,0,0.8,0,0.2,0,0.8,0
62+
61,248,248,Poisson,0.33333,NA,NA,NA,0.7,0,0.3,0,0.7,0,0.3,0,0.7,0,0.3,0,0.7,0,0.3,0
63+
62,250,250,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
64+
63,252,252,Poisson,0.33333,NA,NA,NA,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0
65+
64,256,256,Poisson,0.33333,NA,NA,NA,0.1,0,0.9,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
66+
65,258,258,Poisson,0.33333,NA,NA,NA,0,0.15,0,0.85,0,0.15,0,0.85,0,0.15,0,0.85,0,0.15,0,0.85
67+
66,259,259,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.85,0,0.15
68+
67,260,260,Poisson,0.33333,NA,NA,NA,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0
69+
68,267,267,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
70+
69,273,273,Poisson,0.33333,NA,NA,NA,0.7,0,0.3,0,0.7,0,0.3,0,0.7,0,0.3,0,0.7,0,0.3,0
71+
70,276,276,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.75,0,0.25,0,0.95,0,0.05,0
72+
71,283,283,Poisson,0.33333,NA,NA,NA,0,0.05,0,0.95,0,0.1,0,0.9,0,0.05,0,0.95,0,0.05,0,0.95
73+
72,285,285,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
74+
73,286,286,Poisson,0.33333,NA,NA,NA,0,0.05,0,0.95,0,0.1,0,0.9,0,0.05,0,0.95,0,0.05,0,0.95
75+
74,291,291,Poisson,0.33333,NA,NA,NA,0,0.05,0,0.95,0,0.1,0,0.9,0,0.05,0,0.95,0,0.05,0,0.95
76+
75,297,297,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
77+
76,301,301,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
78+
77,304,304,Poisson,0.33333,NA,NA,NA,0.95,0,0,0.05,0.95,0,0,0.05,0.95,0,0,0.05,0.95,0,0,0.05
79+
78,305,305,Poisson,0.33333,NA,NA,NA,0.9,0,0.1,0,0.9,0,0.1,0,0.9,0,0.1,0,0.9,0,0.1,0
80+
79,307,307,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
81+
80,318,318,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
82+
81,319,319,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
83+
82,322,322,Poisson,0.33333,NA,NA,NA,0.25,0,0.75,0,0.25,0,0.75,0,0.25,0,0.75,0,0.25,0,0.75,0
84+
83,325,325,Poisson,0.33333,NA,NA,NA,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1
85+
84,328,328,Poisson,0.33333,NA,NA,NA,0.2,0,0.8,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
86+
85,329,329,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
87+
86,333,333,Poisson,0.33333,NA,NA,NA,0.2,0,0.8,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
88+
87,334,334,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
89+
88,337,337,Poisson,0.33333,NA,NA,NA,0.2,0,0.8,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
90+
89,342,342,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
91+
90,345,345,Poisson,0.33333,NA,NA,NA,0,0.65,0,0.35,0,0.65,0,0.35,0,0.65,0,0.35,0,0.65,0,0.35
92+
91,348,348,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.85,0,0.15
93+
92,353,353,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.85,0,0.15
94+
93,354,354,Poisson,0.33333,NA,NA,NA,0,0.05,0.95,0,0,0.1,0.9,0,0,0.35,0.65,0,0,0.05,0.95,0
95+
94,359,359,Poisson,0.33333,NA,NA,NA,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0
96+
95,364,364,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
97+
96,368,368,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
98+
97,369,369,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
99+
98,372,372,Poisson,0.33333,NA,NA,NA,0,0.35,0,0.65,0,0.35,0,0.65,0,0.35,0,0.65,0,0.35,0,0.65
100+
99,375,375,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
101+
100,376,376,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
102+
101,377,377,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
103+
102,378,378,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
104+
103,382,382,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
105+
104,393,393,Poisson,0.33333,NA,NA,NA,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95
106+
105,395,395,Poisson,0.33333,NA,NA,NA,0,0.99,0,0.01,0,0.99,0,0.01,0,0.99,0,0.01,0,0.99,0,0.01
107+
106,396,396,Poisson,0.33333,NA,NA,NA,0.99,0,0.01,0,0.99,0,0.01,0,0.99,0,0.01,0,0.99,0,0.01,0
108+
107,400,400,Poisson,0.33333,NA,NA,NA,0.99,0,0.01,0,0.99,0,0.01,0,0.99,0,0.01,0,0.99,0,0.01,0
109+
108,408,408,Poisson,0.33333,NA,NA,NA,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1
110+
109,423,423,Poisson,0.33333,NA,NA,NA,0.01,0,0.99,0,0.01,0,0.99,0,0.01,0,0.99,0,0.01,0,0.99,0
111+
110,424,424,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
112+
111,426,426,Poisson,0.33333,NA,NA,NA,0,0.95,0.05,0,0,0.95,0.05,0,0,0.95,0.05,0,0,0.95,0.05,0
113+
112,434,434,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
114+
113,439,439,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
115+
114,446,446,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05
116+
115,448,448,Poisson,0.33333,NA,NA,NA,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95
117+
116,452,452,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
118+
117,462,462,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
119+
118,465,465,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
120+
119,471,471,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
121+
120,474,474,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
122+
121,480,480,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05
123+
122,483,483,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
124+
123,485,485,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
125+
124,486,486,Poisson,0.33333,NA,NA,NA,0,0.9,0,0.1,0,0.9,0,0.1,0,0.9,0,0.1,0,0.9,0,0.1
126+
125,487,487,Poisson,0.33333,NA,NA,NA,0.9,0.05,0.05,0,0.9,0.05,0.05,0,0.9,0.05,0.05,0,0.9,0.05,0.05,0
127+
126,495,495,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
128+
127,500,500,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05
129+
128,504,504,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
130+
129,510,510,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.9,0,0.1
131+
130,512,512,Poisson,0.33333,NA,NA,NA,0.05,0.92,0,0.03,0.05,0.92,0,0.03,0.05,0.92,0,0.03,0.05,0.92,0,0.03
132+
131,513,513,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05
133+
132,515,515,Poisson,0.33333,NA,NA,NA,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0
134+
133,516,516,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
135+
134,519,519,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
136+
135,521,521,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
137+
136,528,528,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
138+
137,531,531,Poisson,0.33333,NA,NA,NA,0.95,0,0,0.05,0.95,0,0,0.05,0.95,0,0,0.05,0.95,0,0,0.05
139+
138,534,534,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
140+
139,537,537,Poisson,0.33333,NA,NA,NA,0,1,0,0,0,1,0,0,0,1,0,0,0,0.35,0,0.65
141+
140,538,538,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
142+
141,542,542,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
143+
142,549,549,Poisson,0.33333,NA,NA,NA,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95
144+
143,550,550,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.8,0,0.2,0,0.95,0,0.05,0
145+
144,555,555,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05
146+
145,557,557,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
147+
146,559,559,Poisson,0.33333,NA,NA,NA,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0
148+
147,564,564,Poisson,0.33333,NA,NA,NA,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0
149+
148,570,570,Poisson,0.33333,NA,NA,NA,0.95,0,0,0.05,0.95,0,0,0.05,0.95,0,0,0.05,0.95,0,0,0.05
150+
149,571,571,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05
151+
150,576,576,Poisson,0.33333,NA,NA,NA,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95
152+
151,583,583,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
153+
152,584,584,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05
154+
153,585,585,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
155+
154,586,586,Poisson,0.33333,NA,NA,NA,0.15,0,0.85,0,0.15,0,0.85,0,0.15,0,0.85,0,0.15,0,0.85,0
156+
155,587,587,Poisson,0.33333,NA,NA,NA,0.15,0,0.85,0,0.15,0,0.85,0,0.15,0,0.85,0,0.15,0,0.85,0
157+
156,588,588,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
158+
157,589,589,Poisson,0.33333,NA,NA,NA,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1
159+
158,590,590,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
160+
159,594,594,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05
161+
160,599,599,Poisson,0.33333,NA,NA,NA,0,0.25,0,0.75,0,0.25,0,0.75,0,0.25,0,0.75,0,0.25,0,0.75
162+
161,601,601,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
163+
162,609,609,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
164+
163,610,610,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
165+
164,614,614,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05
166+
165,615,615,Poisson,0.33333,NA,NA,NA,0,0.05,0.95,0,0,0.05,0.95,0,0,0.05,0.95,0,0,0.05,0.95,0
167+
166,616,616,Poisson,0.33333,NA,NA,NA,0.95,0.05,0,0,0.95,0.05,0,0,0.95,0.05,0,0,0.95,0.05,0,0
168+
167,617,617,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
169+
168,618,618,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
170+
169,624,624,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05
171+
170,626,626,Poisson,0.33333,NA,NA,NA,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05
172+
171,629,629,Poisson,0.33333,NA,NA,NA,0,0.5,0.5,0,0,0.5,0.5,0,0,0.5,0.5,0,0,0.5,0.5,0
173+
172,630,630,Poisson,0.33333,NA,NA,NA,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0
174+
173,631,631,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
175+
174,632,632,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
176+
175,633,633,Poisson,0.33333,NA,NA,NA,0.25,0,0.75,0,0.25,0,0.75,0,0.25,0,0.75,0,0.25,0,0.75,0
177+
176,639,639,Poisson,0.33333,NA,NA,NA,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0
178+
177,643,643,Poisson,0.33333,NA,NA,NA,0.05,0.94,0.005,0.005,0.05,0.94,0.005,0.005,0.05,0.94,0.005,0.005,0.05,0.94,0.005,0.005
179+
178,644,644,Poisson,0.33333,NA,NA,NA,0.85,0,0,0.15,0.85,0,0,0.15,0.85,0,0,0.15,0.85,0,0,0.15
180+
179,648,648,Poisson,0.33333,NA,NA,NA,0.97,0,0.03,0,0.97,0,0.03,0,0.97,0,0.03,0,0.97,0,0.03,0
181+
180,651,651,Poisson,0.33333,NA,NA,NA,0.97,0.03,0,0,0.65,0.35,0,0,0.97,0.03,0,0,0.97,0.03,0,0
182+
181,654,654,Poisson,0.33333,NA,NA,NA,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95
183+
182,655,655,Poisson,0.33333,NA,NA,NA,0.97,0,0.03,0,0.97,0,0.03,0,0.97,0,0.03,0,0.97,0,0.03,0
184+
183,659,659,Poisson,0.33333,NA,NA,NA,0.97,0,0.03,0,0.97,0,0.03,0,0.97,0,0.03,0,0.97,0,0.03,0
185+
184,660,660,Poisson,0.33333,NA,NA,NA,0.15,0,0.85,0,0.15,0,0.85,0,0.15,0,0.85,0,0.15,0,0.85,0
186+
185,661,661,Poisson,0.33333,NA,NA,NA,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95,0,0.05,0,0.95
187+
186,662,662,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
188+
187,668,668,Poisson,0.33333,NA,NA,NA,0.97,0,0.03,0,0.97,0,0.03,0,0.97,0,0.03,0,0.97,0,0.03,0
189+
188,669,669,Poisson,0.33333,NA,NA,NA,0.97,0.03,0,0,0.97,0.03,0,0,0.97,0.03,0,0,0.97,0.03,0,0
190+
189,671,671,Poisson,0.33333,NA,NA,NA,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0
191+
190,672,672,Poisson,0.33333,NA,NA,NA,0.97,0,0.03,0,0.97,0,0.03,0,0.97,0,0.03,0,0.97,0,0.03,0
192+
191,675,675,Poisson,0.33333,NA,NA,NA,0,0.15,0,0.85,0,0.15,0,0.85,0,0.15,0,0.85,0,0.15,0,0.85
193+
192,679,679,Poisson,0.33333,NA,NA,NA,0,0.97,0,0.03,0,0.97,0,0.03,0,0.97,0,0.03,0,0.97,0,0.03

‎default_Parameter_Files_Apollo/convert_Files/Recombination_hotspots_to_JSON.csv‎

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Original file line numberDiff line numberDiff line change
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1+
Hotspot_ID,Start,Stop,Probability,Selectivity
2+
1,24,66,0.07818,1
3+
2,67,102,0.0666,1
4+
3,103,132,0.0558,1
5+
4,133,177,0.0828,1
6+
5,178,222,0.0828,1
7+
6,223,276,0.099,1
8+
7,277,321,0.08217,1
9+
8,322,360,0.072,1
10+
9,361,417,0.1044,1
11+
10,418,462,0.08226,1
12+
11,463,516,0.099,1
13+
12,517,567,0.0936,1
14+
13,568,618,0.0936,1
15+
14,619,669,0.09417,1

‎default_Parameter_Files_Apollo/parameters_Example/parameters_MASTER.json‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -44,22 +44,22 @@
4444
# Haplotype retriever and count extractor
4545
# ALL for NODE ID to get the sequence haplotypes for all infected individual_Profiles
4646
# OR list the nodes seperated by a comma to get the haplotype frequency for those individuals
47-
"Haplotype Node IDs":"8_8",
47+
"Haplotype Node IDs":"0_0",
4848

4949
# Pedigree search
5050
"Pedigree Node ID":"0_0",
5151
"Pedigree Tissue":"Plasma",
5252
"Pedigree Generation":52,
53-
"Pedigree Sequence":"test_Folder/pedigree/one.fasta",
53+
"Pedigree Sequence":"reference_Genomes/reference_1.fasta",
5454
"Pedigree get Sequences":"Yes",
5555

5656
# Base site model or recombination hotspots to JSON script (File has to be tab delimited)
57-
"Convert file location":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Simulator_Linux/Mutation_Site_model_covid_full.csv",
57+
"Convert file location":"convert_Files/Recombination_hotspots_to_JSON.csv",
5858

5959
# Convert pedigree folder to R format
60-
"Pedigree folder location":"/mnt/d/Deshan/Books/University of Calgary/Experiments/Simulator_Linux/resultsHIV_2/node_Data/0_0/pedigree_Information/one",
60+
"Pedigree folder location":"results/node_Data/0_0/pedigree_Information/one",
6161

62-
"Segregating match sequences":"/mnt/d/Deshan/Books/University of Calgary/Experiments/HIV Simulation/patient_14/Full_analysis/Clean_name/last_Gen/merged.fasta",
62+
"Segregating match sequences":"reference_Genomes/reference_1.fasta",
6363
"Segregating match Node ID":"0_0",
6464
"Segregating match tissue":"Plasma",
6565
"Segregating match cutoff":"0.96875"

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