Global symbol requires explicit package name issue

Question

[apulunuj]

I have really little background on perl. Currently, I am trying to make use of the FASTKs pipeline by mrckrain on github. The pipeline works primarily through a bash script called run_kspipeline.sh file. The bash script makes use of a perl script.

When I run the perl script I get the global symbol requires explicit package at the following lines, which are highlighted.

Here is the original script as reference: https://github.com/mrmckain/FASTKs/blob/master/bin/FAST_kspipe_part2.pl

I would appreciate some help with the current issue. The lines where I get the error are lines are where the variable $temp_seqid = $1 within the block. If you check the original code on github, the error come up at lines 74 ,91, 108, and 127.

I would like help in finding a solution to the "Global symbol requires explecit package error".

The script below:

!/usr/bin/perl -w

use strict;

my $qsho = $ARGV[0];

my $ssho = $ARGV[1];

my $setid = substr($ARGV[2], 0, index($ARGV[2], "."));

system "mkdir $qsho\_$ssho\_ks/set$setid";

my $prequery = substr($ARGV[3], 0, index($ARGV[3], "."));

my $prehit = substr($ARGV[4], 0, index($ARGV[4], "."));

my %qindex = index_input($prequery);

my %sindex = index_input($prehit);

my %rqindex = index_input_rev($prequery);

my %rsindex = index_input_rev($prehit);

my ($qseqs, $sseqs, $pepq, $peps) = subset_seqs($ARGV[2],%qindex, %sindex);

#my %qseqs = %$qseqs;

#my %sseqs = %$sseqs;

open my $setfile, "<", $ARGV[2];

while(<$setfile>){

        chomp;
        my ($pair_id, $line_info) = split /,/;
        create_fasta($pair_id, $line_info);
        run_muscle($pair_id);
        run_pal2nal($pair_id);
        create_phyml_aln($pair_id);
        run_paml($pair_id);
        get_kaks_values($pair_id, $line_info);
}

open my $newfile, ">", "$qsho\_$ssho\_ks/$qsho\_$ssho.kaks.2.txt";

print $newfile "Pair\tKa\tKs\tKa/Ks\tSeqQ\tSeqS\n";        

my $home = `pwd`;
print "$home\n";


sub index_input {
    my %index;
    open my $infile, "<", "$qsho\_$ssho\_ks/$_[0].index";

    while(<$infile>){
        chomp;
        my ($new, $old) = split /\s+/;
        $index{$old}=$new;
    }
    return(%index);
} 


sub index_input_rev {
        my %index;
        open my $infile, "<", "$qsho\_$ssho\_ks/$_[0].index";


        while(<$infile>){
                chomp;
                my ($new, $old) = split /\s+/;
                $index{$new}=$old;
        }
        return(%index);
sub subset_seqs {
    my (%qseqs, %sseqs, %pepq, %peps, %fullq, %fulls, %fullpq, %fullps);

    open my $qin, "<", $ARGV[3];
        my $seqid;
        while(<$qin>){
            chomp;
            if(/^>/){
                if(/\s/){
                    />(.*?)\s/;
##74                    $temp_seqid = $1;
                }
                else{
                    $seqid = substr($_, 1);
                }
            }
            else{
                $fullq{$seqid}.=$_;
            }
        }
    open my $sin, "<", $ARGV[4];
        $seqid=();
        while(<$sin>){
            chomp;
            if(/^>/){
                if(/\s/){
                    />(.*?)\s/;
##91                    $temp_seqid = $1;
                }
                else{
                    $seqid = substr($_, 1);
                }
            }
            else{
                $fulls{$seqid}.=$_;
            }
        }
     open my $pqin, "<", $prequery . ".pep";
        $seqid=();
        while(<$pqin>){
            chomp;
            if(/^>/){
                if(/\s/){
                    />(.*?)\s/;
##108                   $temp_seqid = $1;

                }
                else{
                    $seqid = substr($_, 1);
                }
            }
            else{
                $fullpq{$seqid}.=$_;
            }
        }

     open my $psin, "<", $prehit . ".pep";
        $seqid=();
        while(<$psin>){
            chomp;
            if(/^>/){
                if(/\s/){
                    />(.*?)\s/;
##127                   $temp_seqid = $1;
                }
                else{
                    $seqid = substr($_, 1);
                }
            }
            else{
                $fullps{$seqid}.=$_;
            }
        }

[apulunuj]

Thank you @genomax I still not too sure how to enter code properly on biostar. Any pointers? Is it in markdown as well?

[h.mon]

Use the code button to format code, commands and such.

[h.mon]

The problematic pieces of code are the latest changes to the repository, and fairly recent. Maybe you could try with the previous commit.

[popayekid55]

Either remove the use strict from the code or use declare $temp_seqid as my $temp_seqid.use strict` enforces explicit defining the variables before use them

[apulunuj]

I tried both cases, I'm now getting another error uninitialized hash element "sseqid"

[h.mon]

Did you try running FASTKs with the provided example dataset?

[apulunuj]

Yes I did after organizing my directories, I ran it with the dataset and it worked. And I know my input files are the right ones as well. And I don't see any differences with the format of my input files against the example dataset.

[apulunuj]

I have resolved the matter, after investigating the perl script above. I saw that the variable $temp_seqid is necessarily defined outside the block. So it was removed and the script works well again. A fix was pushed to github as well.