Re: feedback on chunk

[David Rio <driodeiros@...>]

No big improvements with your suggestions.
Computing the nt_value only within the conditional reduced the running
time considerably. nt_value is only needed when the expression on the
first conditional evaluates is true.

I started with 5min running time. I am now at 3m 25secs(this and
other improvements). My c version (of the whole tool) takes 45 seconds.

-drd

On Tue, Apr 19, 2011 at 1:37 PM, liam mail <liam.list@googlemail.com> wrote:
>
>> 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
>>
> Are you using LuaJit or have you tried using it? Have you profiled the code?
>
> 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:
>>
>> -------------------------------------------------------------------------
>> 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"])
>> -------------------------------------------------------------------------
>>
>>
>
>