Hello perl monks and wisefolks,

I need some help with a regular expression I have a file that has the following strings that I need to match (Query strings)

file1: GCGAT, CACGT

The target strings are in file2, against which the query strings need to be matched GNGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN GCGANBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB CNCGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

The condition for match is that: 1. Each of the query strings should be matched only in the beginning of the string 2. The query strings can have an N at any position which means for each query string eg. GCGAT we can have NCGAT,GNGAT,GCNAT,GCGNT,GCGAN. So any of these strings should be matched with the target strings. How do I make a regular expression that can contain all the 6 possibilities(includes the original string, GCGAT). I have the following code so far:

# reading in each query string (file1) into an array
while($line1= <INP1>){
chomp($line1);
push (@barcode,$line1);
}

foreach $code(@barcode){
my $filename = $code;
open(OUT, ">$filename") || die "$!\n";
    for my $data(keys %idhash){ # I have stored each of the query stri
+ngs in a hash. The value of the hash contains the target strings. The
+ keys are 1,2,3...
    my $value = $idhash{$data};
    chomp($code);
    
if($value =~ m/^$code/) # HOW DO I WRITE A REGULAR EXPRESSION HERE TO 
+ALLOW ALL THE 6 COMBINATIONS TO BE MATCHED PER QUERY STRING.
            {
        print "$idhash{data}\n"; # where the query string matches the 
+target string print value of the hash
                
            }
        }
    }

[download]
Thanks in advance, biobee

In reply to string match using with an N in any position by biobee07

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