Need fore speed...

Mark Schonewille m.schonewille at economy-x-talk.com
Sat Jul 14 04:34:24 CDT 2007


Ron,

Untested, but I believe you need something like the following:

function findmatches theData,theNumber,theTolerance
   put char 1 to -2 of theNumber into myTempNr
   filter theData with "|*" & tab & "*" & tab & myTempNr & "*" & tab
   set the itemDel to tab
   repeat for each line myLine in theData
     if (item 3 of myLine >= theNumber - theTolerance) and \
     (item 3 of myLine <= theNumber + theTolerance) then
     put myLine & cr after myNewData
   end repeat
   return myNewData
end findMatches

I didn't see any brackets in your e-mail, but I did see a "|" at the  
beginning of each line. Maybe you need to adjust the script for that.

Best regards,

Mark Schonewille

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Op 14-jul-2007, om 9:32 heeft Beynon, Rob het volgende geschreven:

> I don't want to be accused of passing effort out to the list, but I  
> would like to know, from the experts, the fastest way to execute  
> some code..
>
>
>
> I have a file of tab delimited items like so...16,000 lines long  
> read into a single variable. (The right bracket is part of the  
> file, not a quote mark)
>
> <snip data>
>
> I now want to search each line, and match an input number (obsMass)  
> against the third item of each line (pepMass)
>
> If it matches, within a certain tolerance (expressed in parts per  
> million (ppm)  - the tolerance changes with the magnitude of the  
> number) I want to do something with that line. Ties (or multiple  
> hits to the same obsMass) are OK.
>
>
>
> I then want to repeat that process for several thousand different  
> values of obsMass. In other words, I will evaluate the mass  
> matching loop tens of millions of times.
>
>
>
> Some questions - is there advantage in sorting the list by mass first?
>
> Would I gain speed by using integer arithmetic (is that even  
> possible?) or by matching the numbers as strings?
>
>
>
> And most importantly..
>
> Is there an elegant rev way of handling this that I don't even know  
> about?!
>
> Thanks
>
> Rob
>
>
>
>
>
> ________________________________
>
> Prof R J Beynon[h]
> Proteomics and Functional Genomics Group
> Faculty of Veterinary Science
> University of Liverpool
> Crown Street, Liverpool L69 7ZJ
>
> ________________________________
>
> Phone: +44 151 794 4312
>
> Fax: +44 151 794 4243
>
> Email: r.beynon at liv.ac.uk
>
> http://www.liv.ac.uk/pfg
>
> ________________________________
>
>
>
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