Need fore speed...

viktoras didziulis viktoras at ekoinf.net
Sat Jul 14 04:49:36 CDT 2007


Rob,

use the filter:
1) Modify your table so that each line starts with line number as the 
first item;
2) Copy the original table variable (say it is called myTable) to 
tableCopy. Filter modifies contents of variable, so make sure it won't 
touch the original data;
3) use the filter like this:
    filter tableCopy with  *2267.10*
4) now all lines that contain anything between 2267.1000 and 2267.1099 
are stored in tableCopy
5) as these lines contain line numbers too (that's what step 1 was used 
for), now you can cycle through the 1st item of each line in the result 
and find line numbers of the original data that matched the criteria:

set the itemdelimiter to tab
repeat for each line myFilteredLine in tableCopy
    put item 1 of myFilteredLine into lineNo
    put line lineNo of myTable into varModifiedLine
        #modify varModifiedLine contents here
    put varModifiedLine into line lineNo of myTable
end repeat

6) you can put multiple obsMass values and corresponding modifications 
into a variable (e.g. varObsMass) as tab delimited list:
*2267.10*   modified_string_1
*2267.11*   modified_string_2
...
*2271.16*   modified_string_n

and then cycle through each pair of pepMass value and a corresponding 
modification string:

set the itemdelimiter to tab
repeat for each line myConstraintsLine in varObsMass
    put item 1 of myConstraintsLine into varConstraint
    put item 2 of myConstraintsLine into varModifiedLine
    put myTable into tableCopy
    filter newVar with varConstraint

    repeat for each line myFilteredLine in tableCopy
        put item 1 of myFilteredLine into lineNo
        put varModifiedLine into line lineNo of myTable
    end repeat

end repeat

Best wishes!
Viktoras

Beynon, Rob wrote:
>
> 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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