Changing the Boundary.out file to:

chr1    3204563    3661775    -
chr1    3204563    3600000    -
chr1    3204500    3660000    -
chr1    3204000    3204001    -
chr1    3204563    3760000    -

[download]

better illustrates the point. There are 3 instances where I should get a positive result for the first line in DB.out. However, rather than counting the number of times a hit occurs, the line from DB.out is printed 3 times (each with the count value of "1"):

Xkr4    chr1    3204562    3661779    -    3    457.217    1
Xkr4    chr1    3204562    3661779    -    3    457.217    1
Xkr4    chr1    3204562    3661779    -    3    457.217    1

[download]

I also added a step to reset the count to zero for each loop leaving:

my @file1 = ();
open(FILE, @ARGV[0]) || 
    die ("could not open file @ARGV[0]\n");

    while (my $line = <FILE>) {
    chomp $line;
    my ($chr, $start, $stop) = split(/\t/, $line);
        push @file1, [$chr, $start, $stop];
    }
close FILE;

open(FILE, @ARGV[1])||die ("could not open file @ARGV[1]\n");
    
    while(<FILE>){
        ($Gene,$Chrom,$ModStart,$ModEnd,$Strand,$ExonCount,$SizeKB)= s
+plit;        
        foreach my $line (@file1){
            $Count = 0;
            my ($chr, $start, $stop) = @$line;
            if ($chr eq $Chrom && $start gt $ModStart && $end lt $ModE
+nd){
            $Count++;
            print ("$Gene\t$Chrom\t$ModStart\t$ModEnd\t$Strand\t$ExonC
+ount\t$SizeKB\t$Count\n")
            }    
    }
}

[download]

How do I get it to change the number to 3, and not print 3 times?

In reply to Re^2: Searching and Coutning using 2 files with multiple columns by shart3
in thread Searching and Coutning using 2 files with multiple columns by shart3

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