-
Notifications
You must be signed in to change notification settings - Fork 1
/
params.yml
99 lines (95 loc) · 2.06 KB
/
params.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
# Folder with MSAs in .fa format
PATH_MSAS: /data/analysis-paper/msas/paper/50-pangeblocks
# Format: /path/to/directory/<name-experiment>-<standard/row-maximal>-decomp-<not>-alpha-consistent
PATH_OUTPUT: /data/analysis-paper/paper-experiment-decomposition/sars-cov-2-50-complete
OPTIMIZATION:
OBJECTIVE_FUNCTION:
- "nodes"
- "strings"
- "weighted"
- "depth"
- "depth_and_len"
PENALIZATION: # used only with "weighted" and "depth"
- 1000
MIN_LEN: # used only with "weighted"
# - 15
- 20
# - 25
# - 30
MIN_COVERAGE: # used only with "depth"
- 0.11
# - 0.3
# - 0.5
THRESHOLD_VERTICAL_BLOCKS: # minimum length of vertical blocks to be fixed in the optimal solution
# 50 sequences (ommit complete MSA)
- 1
- 60
- 61
- 84
- 90
- 128
- 158
- 171
- 172
- 202
- 249
- 290
- 366
- 408
- 435
- 439
- 488
- 500
- 610
# # 20 sequences (ommit complete MSA)
# - 1
# - 84
# - 96
# - 102
# - 180
# - 202
# - 234
# - 277
# - 309
# - 364
# - 453
# - 481
# - 659
# - 1036
# - 1137
# - 1246
# 100 sequences (ommit complete MSA)
# - 1
# - 30
# - 31
# - 66
# - 98
# - 107
# - 117
# - 122
# - 128
# - 135
# - 147
# - 200
# - 215
# - 266
# - 269
# - 285
# - 338
# - 382
# - 500
TIME_LIMIT: 240 # time limit to run each ILP (minutes)
LOG_LEVEL: "INFO"
THREADS:
SUBMSAS: 1 # ThreadPoolExecutor; 1 -> for loop
ILP: 8 # gurobi threads
DECOMPOSITION:
STANDARD: True
ALPHA_CONSISTENT: False
USE_WILDPBWT: True
# When spliting the MSA into subMSAs, they will have at most this number of cells/positions
# this will limit the number of constraints used by the ILP. Eg: 100 rows x 1000 columns = 100000 positions
MAX_POSITIONS_SUBMSAS: 100000 # 200000 Row-maximal | 100000 Complete
# Maximal blocks with at least the following number of rows and columns will be fixed in the solution
MIN_ROWS_FIX_BLOCK: 0
MIN_COLS_FIX_BLOCK: 0