feedback on chunk
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- Subject: feedback on chunk
- From: David Rio Deiros <driodeiros@...>
- Date: 2011年4月19日 10:58:35 -0500
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:
-------------------------------------------------------------------------
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)
nt_value = sub_read:sub(fs+1, fs+1)
sub_read = sub_read:sub(1, fs) .. "N" .. sub_read:sub(fs+2)
print("Trying: " .. sub_read)
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
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"])
-------------------------------------------------------------------------
My next step is to implement slide_over_read in C, but prior to that I thought you guys
may have some ideas on how to improve it.
That chunk will be called million of times, that's why I want to squeeze as many cpu
cycles as possible.
-drd