in reply to Re^2: Reading two files, cmp certain cols
in thread Reading two files, cmp certain cols

Hi Jethro,

If I want to add a simple counter to count the number of lines in the output (print statement) do you know what it correct way. I pushed one of the variables into an array and counted used the scalar as a counter. But I think there should be a better way. 


while(<INPUT2>){
         chomp;
          my @current_line  = split /\t/;
          push (@{$file2{$current_line[1]}}, $current_line[2]);
          if (exists $file1{$current_line[1]} ) {
               my $key = $current_line[1];
                  foreach my $position1 (@{$file1{$key}}){
          if ($current_line[1] eq $key) {
              if ($current_line[2] == $position1) {
                  if ($current_line[5] ==1) {
                      if ($current_line[14] >= 3){
               print RESULTS join ("\t", $current_line[1],$current_lin
+e[2],$current_line[5],$current_line[14], "***",$key, $position1), "\n
+";
          push (@true_positives, $current_line[1]);

                   }
                }
              }
           }
        }
    }
}

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Re^4: Reading two files, cmp certain cols
by jethro (Monsignor) on Sep 19, 2008 at 23:39 UTC

    Counting needs two steps: Setting the counter to 0 before the loop and the incrementing step:

    #Initialize the counter before the loop
my $true_positives=0;

while(<INPUT2>){
...

          #instead of the push
          $true_positives++;

    [download]

    That's it, $true_positives has the number of positive results after the loop

[reply]
[d/l]
      Hi Jethro,

      In the following loop, I am going to check if ($current_line14 >= 3) then I want to fake around $current_line2 plus/minus 8. Then check if 

      $current_line[1] eq $key 
&& $current_line[5] == 1
&& $current_line [2] = $position1) {

      [download]
      I did the following and again it is loop within a loop and makes it to print a lot of redundant stuff.

      I appreciate any help or solution.

      Pedro 

      
my $from = 0;
my $to =0;
my @range =();

while(<INPUT2>){
         chomp;
          my @current_line  = split /\t/;
          if (exists $file1{$current_line[1]} ) {
               my $key = $current_line[1];
                  foreach my $position1 (@{$file1{$key}}){
                        if ($current_line[14] >= 3){
                   $from = $current_line[2]-8;
                   $to = $current_line[2]+8;
                    for ($from .. $to){
                    push (@range, $_);
                    }
                  }
             foreach my $pos (@range){
                 if ($pos = $position1) {
             if  (    $current_line[1] eq $key
                   && $current_line[5] == 1
                  )
             {
print join ("\t", $current_line[1],$current_line[2],$current_line[5],$
+current_line[14], "***",$key, $position1), "\n";
          $true_positives++;
          push (@{$file2{$current_line[1]}}, $current_line[5]);
             }
          }
        }
    }
}

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[reply]
[d/l]
[select]

        "fake" is definitely the wrong word. So I can only guess what you want to do from your code. You seem to check if $position1 is between $current_line2-8 and $current_line2+8. In that case you have a bug in your code, in the line if ($pos = $position1) { the '=' should have been a '=='. Furthermore the loop isn't necessary, you only need two comparisions instead: 

        #                   $from = $current_line[2]-8;
#                   $to = $current_line[2]+8;
#                    for ($from .. $to){
#                    push (@range, $_);
#                    }
#                  }
#             foreach my $pos (@range){
#                 if ($pos == $position1) {
# substitute with
                 if ($position1>=$current_line[2]-8 and
                     $position1<=$current_line[2]+8) {

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