Re: Help with function, count matches and store in hash & retrieve sorted

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.

Comment on Re: Help with function, count matches and store in hash & retrieve sorted Download Code

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Re^2: Help with function, count matches and store in hash & retrieve sorted by Marshall (Canon) on Jul 03, 2017 at 01:49 UTC
Ok, what would be the most helpful is just the data structures that are used in the call to `match_query($indexfile,$queryseq);` and which re-produce the problem. I guess?: `my $indexfile = { 'GCTCAGGA' => '4', 'AGCGTAGC' => '5', 'TTCTGCCT' => '3', 'CATGCCTA' => '6', 'TCGCCTTA' => '1', 'GTAGAGAG' => '7', 'GCGTAAGA' => '13', 'TAGATCGC' => '9', 'CTAGTACG' => '2', 'CTAAGCCT' => '16', 'CTCTCTAT' => '10', 'ACTGCATA' => '14', 'AGAGTAGA' => '12', 'TATCCTCT' => '11', 'AAGGAGTA' => '15', 'CCTCTCTG' => '8' };` [download] What is the $queryseq that goes with that table? What the heck does: "along with input files that are added as I iterate over a while loop" mean? You are asking a question about an error that you are getting in a subroutine. In the best case, you provide a complete set of runnable code. All we have to do is download and hit the "run" button to replicate exactly your problem. What we have now is kind of like a UFO report. If the problem can be reproduced (seen) by all, then there will be solutions forthcoming. Your job is to boil this down to a single set of inputs that "demo's the problem". If the $indexfile structure above doesn't need 16 entries to demo the problem, then use fewer entries. Sometimes submitting an excellent "bug" report requires a lot of work to get the situation down to a minimal, easily replicate-able situation. I have certainly spent entire work weeks doing that for complex issues.	[reply] [d/l] [select]
Re^2: Help with function, count matches and store in hash & retrieve sorted by huck (Prior) on Jul 03, 2017 at 02:03 UTC
I am not sure how I would print my entire list of query strings. How about just when there is a problem `... my $max_count = shift @array; unless (defined ($max_count)) { print "queryseq = \|\|\|$queryseq\|\|\|\n"; print Dumper($indexfile); exit; } my $element; $element->{bar} = $key; $element->{max} = $max_count; push @match_count, $element; ....` [download]	[reply] [d/l]
Re^2: Help with function, count matches and store in hash & retrieve sorted by AnomalousMonk (Archbishop) on Jul 03, 2017 at 12:51 UTC
`if($#array){ $indexfile->{$array[1]} = $array[0]; }` [download] There may be a problem here. The statement `$indexfile->{$array[1]} = $array[0];` will be executed if the `@array` array is empty (`$#array == -1`; -1 is true), or if the `@array` array has two or more elements (`$#array > 0`). Is this what you want? (See discussion of the `$#` sigil (e.g., `$#array`) in perldata.) Give a man a fish: `<%-{-{-{-<`	[reply] [d/l] [select]