Re^2: Searching and Coutning using 2 files with multiple columns

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?

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Re^3: Searching and Coutning using 2 files with multiple columns by kennethk (Abbot) on Sep 16, 2009 at 18:10 UTC
If you want to aggregate results, you need to specify what you are aggregating by. What are you trying to count? Based on what you've written, I will guess you want to know the number of lines of Boundary.out that match each line of DB.out. You can accomplish this by just moving your counter and print statements outside of the foreach loop: `my $Count = 0; foreach my $line (@file1){ my ($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$ExonCount +\t$SizeKB\t$Count\n");` [download]	[reply] [d/l]

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Re^3: Searching and Coutning using 2 files with multiple columns
by kennethk (Abbot) on Sep 16, 2009 at 18:10 UTC

        my $Count = 0;
        foreach my $line (@file1){
            my ($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$ExonCount
+\t$SizeKB\t$Count\n");
[download]

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