Re: Question on loops

Each iteration of your while loop overwrites the variables $V1 and $V2, so by the time your while loop is complete, only the final line's values are there.

Something like this (untested) should work:

use Bio::SeqIO;

my (%all_V1, %all_V2); # hashes to store $V1 and $V2
open (LIST1, "list");
while (<LIST1>) {
    ($V1, $V2) = split /\t/;
    $all_V1{$V1}++; # FIX: this line and the next were originally
    $all_V2{$V2}++; #      incorrectly prefixed with "push".
}
close(LIST1);

my $seqIO_object = Bio::SeqIO->new(-file=>"infile.gb");
my $seq_object = $seqio_object ->next_seq;

for my $feat_object ($seq_object->get_SeqFeatures){
    if ($feat_object->primary_tag eq "CDS"){
        if ($feat_object->has_tag('locus_tag')){
            for my $V3 ($feat_object ->get_tag_values('locus_tag')){
                if (exists $all_V1{$V3}){
                    print "locus_tag: ", $V3, " is unique\n";
                }
            } 
         }
     }
}
[download]

By the way, $V1, $V2 and $V3 are very badly named variables. If you want to be able to come back to your code in a few months and fix a bug, it really helps if your variables have useful names.

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Re^2: Question on loops by Bforde (Initiate) on Dec 12, 2011 at 15:04 UTC
Hello tobyink Thank you for the quick response. I figured that V1 and V2 were being over written had started to look at hashes. I understand what they are doing but not how to use them correctly the code does have an error Type of arg 1 to push must be array (not postincrement (++)) at test.pl line 10, near "++;" Type of arg 1 to push must be array (not postincrement (++)) at test.pl line 10, near "++;" must the V1 and V2 variables be changed to arrays before being added to the hash Brian I can assure you that my actual variable have appropriate names	[reply]
Re^3: Question on loops by tobyink (Canon) on Dec 12, 2011 at 17:48 UTC
Meh. Remove the two `push`es. Should just be: `while (<LIST1>) { ($V1, $V2) = split /\t/; $all_V1{$V1}++; $all_V2{$V2}++; }` [download] ... the `push`es were left overs from an earlier response I typed up but didn't submit, which used arrays. I'll correct the code in my original answer too.	[reply] [d/l] [select]