Re: Hash making

[friedo]

my $snp_covered{$mismatch}= $snp_chip_covered; ...doesn't make sense.

You'll need to declare your hash as a lexical (my) variable outside the loop, so it won't get clobbered each time through. Then you can add keys to it in the normal way.

However, I don't quite understand what you're trying to do with %snp_covered. You're using the same key each time ($mismatch, which is 3) and overwriting the previous value each time there's a match. If you just want to keep track of the total number of matches, you can use a plain scalar and just increment it each time:

my $count;
while(<INPUT2>){
         chomp;
          my @current_line  = split /\t/;
          my $mismatch =3;
          next unless $current_line[5] == 1 && 
            $current_line[14] >= $mismatch;

          $count++;
}

[sesemin]

Thanks Friedo,

I think was not clear enough. I just put $mismatch = 3 to test if I can create a loop. So at each $mismatch, I will have a series of line extracted let's say 1000000 for $mismatch =1.

Then when mismatch changes to 2, another set of lines will be extracted. let's say 700000.

The goal is to have has with keys = different $mismatches and values number of lines extracted.

Any further help is appreciated.

[ikegami]

So at each $mismatch

I don't understand "being at a variable".

I will have a series of line extracted let's say 1000000 for $mismatch =1.

How do you determine how many lines to extract?

Then when mismatch changes to 2, another set of lines will be extracted. let's say 700000.

What causes $mismatch to change?

I will have a series of line extracted

I don't understand "extracting a line". Do you mean "reading a line"? What do with the lines you've extracted?

[sesemin]

Let's look at the following code. Up to counter1++ and forget the rest for now. with the conditions set (unless), I am taking those lines that are qualified. Counter1 gives me the number of counts for those lines (value for a hash). If I can iterate through $current_line14 >= and change the value of 3 (which is fixed here) I will get different counts. Therefore by each change at value of current_line14 >= you will get a different count. So your hash keys become your loop values from 3..30 for example and values will be the number of lines extracted. If I want to change "3" manually I have to perform the while loop 20 - 30 times for each key in order to get the counts.

while(<INPUT2>){
         chomp;
          my @current_line  = split /\t/;
     
          # eliminate unqualified lines early
     
next unless $current_line[5] == 1 && $current_line[14] >= 3;
         
          $counter1++;

     if ($file1{ $current_line[1]}) {
     my ($from, $to) = @{ $file1{ $current_line[1] } };
for ($from <= $current_line[2] && $current_line[2] <= $to) {

   print join("\t", $current_line[1],$current_line[5],$current_line[14
+], "***",$current_line[2]), "\n";

           $lines++;
            }
      }
}