Use of uninitialized value error in Perl Script
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0
Entering edit mode
3.5 years ago
apulunuj ▴ 30

I am making use of a perl script for a pipeline and I'm getting the following error message. I don't know what to do. The error message I'm getting is:

Use of uninitialized value $qulen in division (/) at FAST_kspipe.pl line 167, <$blast_file> line 7. Illegal division by zero at FAST_kspipe.pl line 167, <$blast_file> line 7.

The perl script can be found here:

https://github.com/mrmckain/FASTKs/blob/master/FAST_kspipe.pl

If you can't access it here is the code with the line (the line of interest is , next if (abs(($qend-$qstart)*3)/$qulen) < 0.75 || (abs(($hend-$hstart)*3)/$sublen) < 0.75; )

sub get_quality_pairs_ORIG {
    my %hits;
        my %gene_hits;
    my (%sseqs, %qseqs);
    my $temp_seqid;
    open my $qfile, "<", $_[1];
    while(<$qfile>){
            chomp;
            if(/>/){
                    $temp_seqid = substr($_, 1);
            }
            else{
                    $qseqs{$temp_seqid}.=$_;
            }
    }
    open my $sfile, "<", $_[2];
    while(<$sfile>){
            chomp;
            if(/>/){
                    $temp_seqid = substr($_, 1);
            }
            else{
                    $sseqs{$temp_seqid}.=$_;
            }
    }

open my $blast_file, "<", $_[0];
open my $outfile, ">", "$qsho\_$ssho\_ks/$qsho\_$ssho.paralogs.txt";
my $current_query = ""; 
while (<$blast_file>) {
    chomp;
    my ($query,$hit,$perc_id,$aln_len, $mismatch, $indel, $qstart,$qend,$hstart,$hend) = split /\s+/;   
    next if ($perc_id >= 100.00);
            next if $query eq $hit;
            #my ($qgene, $sgene);
            #$query =~ /(.+c\d+_g\d+)/;
            #$qgene = $1;
            #$hit =~ /(.+c\d+_g\d+)/;
            #$sgene = $1;

            #next if $qgene eq $sgene;
            my $sublen = length($sseqs{$hit});
            my $qulen = length($qseqs{$query});
            next if (abs(($qend-$qstart)*3)/$qulen) < 0.75 || (abs(($hend-$hstart)*3)/$sublen) < 0.75;
    #next if exists $gene_hits{$sgene}{$qgene} || exists $gene_hits{$qgene}{$sgene};
            #next if exists $hits{$hit}{$query} || exists $hits{$query}{$hit};
            #next if exists $hits{$hit};
            #                #next if exists $hits{$query};
            #                                next if exists $gene_hits{$sgene}{$qgene} || exists $gene_hits{$qgene}{$sgene};
            #                                                next if exists $hits{$hit}{$query} || exists $hits{$query}{$hit};
perl • 3.1k views
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1
Entering edit mode

What's the question ? The error message is pretty clear. The variable $qulen is not defined, i.e. has no value so you can't use it in a division. Now if you want to find out why you're getting this error, check where this variable is supposed to be initialized:
my $qulen = length($qseqs{$query});
so either $query or $qseqs{$query} is not defined. You should also have got at least a warning about this before the error. Since $query seems to be populated by parsing a blast output, check that its format conforms to the expected format. Since the error happens at <$blast_file> line 7, check this line.

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0
Entering edit mode

Thank you I fixed it now, it was the blast format.

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