One way to do this is to capture the junk along with the substrings: 
#! /usr/bin/perl -w
use strict;

my (@genes, @positions);
my $screen = "ATCGATCGXXXXXATCGATXXXACTGCTACGGTACXXXAATTATXGCGCGXXT";

if ($screen =~ /X/) {
   my @parts = split /(X+)/, $screen;
   my $pos = 0;
   foreach my $part (@parts) {
      if ($part !~ /X/) {
         push @genes, $part;
         push @positions, $pos;
         print "Gene $part is at position $pos\n";
      }
      $pos += length $part;
   }
   my $genecounter = @genes;
   print "Number of components  = $genecounter\n\n";
}

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-Mark

In reply to Re: Split Function - Positions by kvale
in thread Split Function - Positions by MiamiGenome

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