Could you provide perhaps a single line or maybe even 2 or 3 of the input file?

I modified your code a bit for brevity(untested). I am not all that familiar with microbiology(been 35 years since high school biology). I suspect there are CPAN modules that will handle problems like this. Do a search for like this one at bio:: and see if there might be something you can use if that is an option for you.

Hope that is in some way helpful... 

#!/usr/bin/perl
use strict;
use warnings;
print "Select the region where you want to find CpG Island\n";
my ($a,$t,$c,$g,$cg,$total);
print  "1. Region 1-200\n";
print  "2. Region 2-202\n";
print  "3. Region 3-203\n";
my $choice =<STDIN>;
chomp($choice);
my $file = 'd:\perl\1.txt';

if ( $choice == 1 ) {
   region(0);
} elsif ( $choice == 2 ) {
   region(1);
} elsif ( $choice == 3) {
   region(2);
}

sub region {
    my $start = shift;
    open(INPUT, $file) or die ("File not found");
    foreach(my $line = <INPUT>) {
        my $a = substr($line,$start,200) =~ tr/A//;
        my $t = substr($line,$start,200) =~ tr/T//;
        my $g = substr($line,$start,200) =~ tr/G//;
        my $c = substr($line,$start,200) =~ tr/C//;
        my $cg = substr($line,$start,200) =~ tr/ CG //;
        my $total = substr($line,$start,200) =~ tr/ATGC//;
    }
}

my $CpG = ($cg)/$total*100;
print"Count of A = $a\n";
print"Count of T = $t\n";
print"Count of G = $g\n";
print"Count of C = $c\n";
print"CG = $cg\n";
print"total count of ATGC = $total\n";
print"CpG percentage = $CpG\n";

if ($CpG>=60) {
    print"CpG present";
} else {
    print"CpG absent";
}

[download]
Update: moved printing back outside the sub. What I get for messing with code at this hour of the morning...
...the majority is always wrong, and always the last to know about it...
Insanity: Doing the same thing over and over again and expecting different results...
wjw

In reply to Re^15: how to access elements in perl by wjw
in thread how to access elements in perl by grewal7634

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.