to make my input files I used the following code:

sub get_index(){
    my $file = shift;
    my $indexfile;
    open FILE,$file;
    while(<FILE>){
        chomp;
        my @array = split /\,/,$_;
        if($#array){
            $indexfile->{$array[1]} = $array[0];
        }
    }
    close FILE;
    
    return $indexfile;

[download]

on a .txt file that looks like this :
1,TCGCCTTA
2,CTAGTACG
3,TTCTGCCT
4,GCTCAGGA
5,AGCGTAGC
6,CATGCCTA
7,GTAGAGAG
8,CCTCTCTG
9,TAGATCGC
10,CTCTCTAT
11,TATCCTCT
12,AGAGTAGA
13,GCGTAAGA
14,ACTGCATA
15,AAGGAGTA
16,CTAAGCCT
along with input files that are added as I iterate over a while loop. These files look like:
p1='CTAAGCCT'
I suppose its possible that p1 is occasionally an empty string, I am not sure how I would print my entire list of query strings.
please let me know if you need more information.

In reply to Re: Help with function, count matches and store in hash & retrieve sorted by Pathogenomix
in thread Help with function, count matches and store in hash & retrieve sorted by Pathogenomix

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