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substring count in string

Thu, 04/11/2019 - 02:06 am

Hi all,

I am facing a small challenge checking strings with Igor.

I tried to build a function to count all occurrences of a substring (motif) within a string (sequence) using stringmatch.

My string is about 8000 characters long, and I have more than one substring (actually hundreds) to find.

I have to add the beginning of the string to the end as well, so don't wonder why I create the "search_string"

One run takes approximately 30s - do you have any ideas to speed this up?

function find_motif(sequence, motif)
string sequence, motif
string search_string = sequence+sequence[0,strlen(motif)-1]
variable motif_count = 0
variable i = 0
 
for(i=0; i<(strlen(sequence)-1); i+=1)
    if(stringmatch(search_string[i,(i+strlen(motif)-1)], motif))
        //add warning if motif in last part
        if(i>=(strlen(sequence)-strlen(motif)+1))
            print "motif found in end_to_start region"
        endif
        motif_count += 1
        endif
endfor
 
 
return motif_count
end