A .qual file is a numerical representation of the confidence of a nucleotide sequencer. Used by the modern, automated sequencers, they assign a 2 digit value to each nucleotide ACTGU (which are what all DNA is composed of) representing the accuracy of the sequencer guessing at that particular nucleotide (in my case, 40 being = 100% confidence). For example: if I were a DNA sequencer and I KNOW that the first three nucleotides are ACT but I'm only partially confident that the last nucleotide is a G. The .qual file would look something like this: 40 40 40 34. I hope this makes sense! Let me know if you need/would like further explanation!

here's my code:

#!/usr/bin/perl -w

use strict;
use warnings;

use Bio::Seq;
use Bio::SeqIO;
use Bio::Seq::Quality;

my $seq_count = 0;
my $used_seqs;
my $match;
my $front;
my $end;
my $front_tag = 0;
my $end_tag = 0;
my $nfront = 0;
my $nend = 0;
my $no_match = 0;

my $seq_file = "fastaTestData.fna";
my $qual_file = "qualTestData.qual";

my $seqIn_obj = Bio::SeqIO->new(-file => "$seq_file", -format => 'fast
+a') or die "Can't access $seq_file\n";

#creates the fasta output file
print "creating fasta output file\n";
my $fasta = Bio::SeqIO->new(-file => '>testFasta.fasta', -format => 'f
+asta');

# creates new qual output file
print "creating quality output file\n";
my $quality = Bio::SeqIO->new(-file => '>testQual.qual', -format => 'q
+ual');

#reads in the tag file as a fasta file
print "Reading in tag file\n";
my $tag_obj = Bio::SeqIO->new(-file => "mids.fa", -format => 'fasta') 
+or die "Can't access mids.fa\n";

#adds the tag id and sequence into a hash
print "creating tag hash\n";
my %tag_hash = ();
while(my $tag = $tag_obj->next_seq){
    # instantiates the hash map, using the tag id as the key and the t
+ag sequence as the value.
    $tag_hash{$tag->id} = $tag->seq;
}


# reads in the quality files associated with the fasta files.
print "reading in qual file\n";
my $qual_obj = Bio::SeqIO->new(-file => "$qual_file", -format => "qual
+") or die "Can't access $qual_file";

print "creating qual hash\n";

my %qual_hash = ();


while(my $qual_seq = $qual_obj->_next_qual){
    # next line is pushing a reference to an array onto an array of sc
+alar array references
    $qual_hash{$qual_seq->id()} = $qual_seq->qual();
}


# reads in the next sequence (next_seq) and stores it in $seqIn_obj th
+en prints it out.
print "Applying regexs\n";
while (my $seq = $seqIn_obj->next_seq){
    print "getting new sequence\n";
    $seq_count += 1;
    $match = 0;
    $front = 0;
    $end = 0;

    my $temp_seq = $seq->seq;
    

    
    
        while((my $id, my $tag_seq) = each(%tag_hash)){
            print "cycling through tag hash\n";
            
            # reverses the tag_seq
            my $rtag_seq = reverse $tag_seq;    

            for(my $i = 0; $i <= 1; $i += 1){
            
                if($temp_seq =~ s/^$tag_seq//i){
                    print "removing tag\n";
                    $match += 1;
                    $front += 1;
                    $front_tag = 1;
                }

                
                if($temp_seq =~ s/^$rtag_seq//i){
                    print "removing tag\n";
                    $match += 1;
                    $front += 1;
                    $front_tag = 1;
                }

                                if($temp_seq =~ s/$tag_seq$//i){
                    print "removing tag\n";
                    $match += 1;
                    $end += 1;
                    $end_tag = 1;
                }

                
                if($temp_seq =~ s/$rtag_seq$//i){
                    print "removing tag\n";
                    $match += 1;
                    $end += 1;
                    $end_tag = 1;
                }
            }
                
        }
        
        

    if($front > 1){
        $nfront += 1;
    }

    if($end > 1){
        $nend += 1;
    }

    if($match == 0){
        $no_match += 1;
    }

    if($front <= 1 && $end <= 1 && $match != 0){
        print "removing 6 nts and amending qual sequence\n";

        $used_seqs += 1;

        my @qual = @{$qual_hash{$seq->id()}};
        print ("@qual\n");
        my $qual_string = join(" ", @qual);
        print "$qual_string\n";
        $qual_string =~ s///;
        print "$qual_string\n";
        
        if($front_tag == 1){
            $qual_string =~ s/^\w{32}//;
            $temp_seq =~ s/^\w{6}//;
            $front_tag = 0;
        }
        elsif($end_tag == 1){
            $qual_string =~ s/\w{32}$//;
            $temp_seq =~ s/\w{6}$//;
            $end_tag = 0;
        }

        
        
        # creates the new sequence and passes the metadata to the sequ
+ence object
        print "creating fasta seq and writing to file\n";
        my $new_seq = Bio::Seq->new(-seq => $temp_seq, -display_id => 
+$seq->id, -length => $seq->length,
        -desc => $seq->desc, -alphabet => $seq->alphabet);

        # writes the new sequence object to the specified file
        $fasta->write_seq($new_seq);

        print "creating qual seq and writing to file\n";
        my $new_qual = Bio::Seq::Quality->new(-seq => $qual_string, -i
+d => $seq->id(), -desc => $seq->desc);

        $quality->write_seq($new_qual);

        }
}

print("nfront = $nfront\nnend = $nend\nno_match = $no_match\nseq_count
+ = $seq_count\nused_seqs = $used_seqs\n");
[download]

Feel free to ask if anything doesn't make sense (for I may have left something out from the copy and paste), if there are any hints to make it more efficient etc.. most importantly, to fix the error stated previously! Thanks again!