Basically, different arrays have different pieces of information in them and I have to go from one to another to another from that. In this case, I have to go from each element in @Genes and extract its corresponding element from a long file which I read in as @lines. I keep getting a strange error that reads, syntax error at findscaffold.pl line 38, near "$N (" Does anyone know what this is? Here is the code. </p? 


my @Genes = qw(A B C D)
my @ptt = ("19384..003059 0 - - A","203581..39502 0 + - B)
my @contig = ();
my @Coordinates;
my @Number;
my $R;


foreach my $G (@Genes){
    for my $x (0..$#ptt){
        if($ptt[$x] =~ /$G/){
        push(@Coordinates,"$ptt[$x]");
        print "$ptt[$x]\n";}
        
            
                        
                    }
                    }
foreach my $C (@Coordinates){
    push (@Number, split(" ", $C));}
    
    
my %hash = ();
my $file = "scaffold_contig.txt";
open(IN, "<$file") or die "Cannot open file $file\n";
my @lines = <IN>;
foreach  $1 (@lines){
    chomp($1);
    my %columns = split(">", $1);}
close(IN);
print "$lines[1];\n"

foreach my $N (@Number){
    for $R (0..$#lines){
        if($lines[$R] =~ /$N/){
            print "lines[$R]\n"
        }
    }
}

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Here is line 38: foreach my $N (@Number){

In reply to Getting an unknown error by andybshaker

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