On 19 April 2011 16:58, David Rio Deiros
<driodeiros@gmail.com> wrote:
I was wondering if I could get some feedback on the following chunk of
lua code. Since I did not get any replies in my previous email I thought
I'd try to be more specific:
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local function slide_over_read(read, pl)
local i = 1
local ps = 7
local fs = 3
local n_hits = 0
while ps + i <= #read+1 do -- while the window is within the size of the read
sub_read = read:sub(i, ps+i-1)
I do not understand why you do not just set ps to 8 and then increment ps later, instead of the addition in the while and the in the string.sub . I also do not understand why you add one to the size of read and then check for less or equal, why not just drop the addition and check for less than?
nt_value = sub_read:sub(fs+1, fs+1)
sub_read = sub_read:sub(1, fs) .. "N" .. sub_read:sub(fs+2)
Shouldn't both nt_value and sub_read be locals? Is string.format quicker? Does concatenation create more temporary strings?
print("Trying: " .. sub_read)
This line I would almost certainly remove if it is being called as much as you say, io is slow.
if pl[sub_read] then -- We have a probe with that sequence
if not pl[sub_read].hits then -- No previous hits
pl[sub_read].hits = {A=0, C=0, G=0, T=0, N=0}
end
pl[sub_read].hits[nt_value] = pl[sub_read].hits[nt_value] + 1
n_hits = n_hits + 1
end
Maybe cache pl[sub_read] as a local?
i = i + 1
end
return n_hits
end
-- Main
probes = {}
probes["123N567"] = {}
read = "123A56789"
print("hits: " .. slide_over_read(read, probes))
print("--> " .. probes["123N567"].hits["A"])
print("---------------")
probes["345N789"] = {}
read = "12345T789"
print("hits: " .. slide_over_read(read, probes))
print("--> " .. probes["345N789"].hits["T"])
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