-
Notifications
You must be signed in to change notification settings - Fork 2
/
example.py
94 lines (67 loc) · 4.36 KB
/
example.py
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
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
from olivar import build, tiling, save, validate
if __name__ == "__main__":
build(
fasta_path = 'example_input/EPI_ISL_402124.fasta', # Path to the fasta reference sequence.
var_path = 'example_input/delta_omicron_loc.csv', # Optional, path to the csv file of SNP coordinates and frequencies.
# Required columns: "START", "STOP", "FREQ". "FREQ" is considered as 1.0 if empty. Coordinates are 1-based.
BLAST_db = 'example_input/Human/GRCh38_primary', # Optional, path to the BLAST database.
# Note that this path should end with the name of the BLAST database (e.g., "example_input/Human/GRCh38_primary").
out_path = './', # Output directory.
title = 'olivar-ref', # Name of the Olivar reference file [olivar-ref].
threads = 1 # Number of threads.
)
tiling(
ref_path = 'example_output/olivar-ref.olvr', # Path to the Olivar reference file (.olvr).
out_path = './', # Output directory.
title = 'olivar-design', # Name of this design [olivar-design].
max_amp_len = 420, # Maximum amplicon length [420].
min_amp_len = 252, # Minimum amplicon length. 0.9*{max-amp-len} if set as None. Minimum 120.
w_egc = 1, # Weight for extreme GC content [1.0].
w_lc = 1, # Weight for low sequence complexity [1.0].
w_ns = 1, # Weight for non-specificity [1.0].
w_var = 1, # Weight for variations [1.0].
temperature = 60, # PCR annealing temperature [60.0].
salinity = 0.18, # Concentration of monovalent ions in units of molar [0.18].
dG_max = -11.8, # Maximum free energy change of a primer in kcal/mol [-11.8].
min_GC = 0.2, # Minimum GC content of a primer [0.2].
max_GC = 0.75, # Maximum GC content of a primer [0.75].
min_complexity = 0.4, # Minimum sequence complexity of a primer [0.4].
max_len = 36, # Maximum length of a primer [36].
check_var = True, # Filter out primer candidates with variations within 5nt of 3' end [False].
# Setting check_var=True is not recommended when a lot of variations are provided,
# since this would significantly reduce the number of primer candidates.
fP_prefix = '', # Prefix of forward primer. Empty string '' by default.
rP_prefix = '', # Prefix of reverse primer. Empty string '' by default.
seed = 10, # Random seed for optimizing primer design regions and primer dimer [10].
threads = 1, # Number of threads.
)
# save(
# design_out = 'example_output/olivar-design.olvd', # Path to the Olivar design file (.olvd)
# out_path = './', # Output directory.
# )
validate(
primer_pool = 'example_output/olivar-design.csv', # Path to the csv file of a primer pool.
# Required columns: "amp_id" (amplicon name), "fP" (sequence of forward primer), "rP" (sequence of reverse primer), "pool" (pool number, e.g., 1).
pool = 1, # Primer pool number [1].
BLAST_db = 'example_input/Human/GRCh38_primary', # Optional, path to the BLAST database.
# Note that this path should end with the name of the BLAST database (e.g., "example_input/Human/GRCh38_primary").
out_path = './', # Output directory.
title = 'olivar-val', # Name of validation.
max_amp_len = 1500, # Maximum length of predicted non-specific amplicon [1500].
temperature = 60, # PCR annealing temperature [60.0].
threads = 1 # Number of threads.
)
validate(
primer_pool = 'example_output/olivar-design.csv', # Path to the csv file of a primer pool.
# Required columns: "amp_id" (amplicon name), "fP" (sequence of forward primer), "rP" (sequence of reverse primer), "pool" (pool number, e.g., 1).
pool = 2, # Primer pool number [1].
BLAST_db = 'example_input/Human/GRCh38_primary', # Optional, path to the BLAST database.
# Note that this path should end with the name of the BLAST database (e.g., "example_input/Human/GRCh38_primary").
out_path = './', # Output directory.
title = 'olivar-val', # Name of validation.
max_amp_len = 1500, # Maximum length of predicted non-specific amplicon [1500].
temperature = 60, # PCR annealing temperature [60.0].
threads = 1 # Number of threads.
)