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
|
CLINVAR_SIG = {}
CLINVAR_SIG["0"] = 'uncertain'
CLINVAR_SIG["1"] = 'not-provided'
CLINVAR_SIG["2"] = 'benign'
CLINVAR_SIG["3"] = 'likely-benign'
CLINVAR_SIG["4"] = 'likely-pathogenic'
CLINVAR_SIG["5"] = 'pathogenic'
CLINVAR_SIG["6"] = 'drug-response'
CLINVAR_SIG["7"] = 'histocompatibility'
CLINVAR_SIG["255"] = 'other'
CLINVAR_SIG["."] = '.'
function contains(str, tok)
return string.find(str, tok) ~= nil
end
function intotbl(ud)
local tbl = {}
for i=1,#ud do
tbl[i] = ud[i]
end
return tbl
end
function clinvar_sig(vals)
local t = type(vals)
-- just a single-value
if(t == "string" or t == "number") and not contains(vals, "|") then
return CLINVAR_SIG[vals]
elseif t ~= "table" then
if not contains(t, "userdata") then
vals = {vals}
else
vals = intotbl(vals)
end
end
local ret = {}
for i=1,#vals do
if not contains(vals[i], "|") then
ret[#ret+1] = CLINVAR_SIG[vals[i]]
else
local invals = vals[i]:split("|")
local inret = {}
for j=1,#invals do
inret[#inret+1] = CLINVAR_SIG[invals[j]]
end
ret[#ret+1] = join(inret, "|")
end
end
return join(ret, ",")
end
join = table.concat
function check_clinvar_aaf(clinvar_sig, max_aaf_all, aaf_cutoff)
-- didn't find an aaf for this so can't be common
if max_aaf_all == nil or clinvar_sig == nil then
return false
end
if type(clinvar_sig) ~= "string" then
clinvar_sig = join(clinvar_sig, ",")
end
if false == contains(clinvar_sig, "pathogenic") then
return false
end
if type(max_aaf_all) ~= "table" then
return max_aaf_all > aaf_cutoff
end
for i, aaf in pairs(max_aaf_all) do
if aaf > aaf_cutoff then
return true
end
end
return false
end
function div(a, b)
if(a == 0) then return "0.0" end
return string.format("%.9f", a / b)
end
|
