genomeindex.pl

#!/usr/bin/perl
use strict;
use warnings;

my $target="ATcgAGCGTTTCG";
my $line;


open (DATAFILE, " < /home/work/biol/References/hg19/chr2.fa")) or die("error: no such file! \n!);
print $target."\n";

while ($line = <DATAFILE>)
{
$target=uc($line);


my @pos;
@pos[0]=0;
for(my $i=1; $i<=3; $i++){
        @pos[$i] = index($target,"CG",@pos[$i-1]) + 1;
        print "$i\t@pos[$i]\n";
}
}