[Omaha.pm] perl

[Jay Hannah]

On Apr 19, 2012, at 1:59 PM, Klinkebiel, David L wrote:
> In this instance the strand does not make a difference. If you wanted to make the change based on a F (forward) or R (reverse) what would the perl look like. Thanks

At that point the command-line version is a little confusing in my opinion. It looks like this:

   perl -anE 'say join "\t", @F[0,1], ($F[2] eq 'F' ? $F[1] + 50 : $F[1] - 50)' inputfile.txt 

So I'd probably write a little program instead:

   use strict;
   use 5.10.0;
   while (<>) {
      chomp;
      my ($chr, $pos, $strand) = split /\t/;
      if ($strand eq 'F') {
         say join "\t", $chr, $pos, $pos + 50;
      } else {
         say join "\t", $chr, $pos, $pos - 50;
      }
   }

So I could comment it, add more logic, whatever.

HTH,

j