In addition to the earlier comments, I'd suggest changing (as an example)
$count_G = ( $seq =~ tr/G//);
$ratio_G = ($count_G/$len);
# print "\n$ratio_G\n";
$ratio_G = Calculate( 'G' );
Writing the sub Calculate
is left as an exercise to the reader. The advantages are you
- get rid of all of the temporary $count_* variables
- remove duplicated code
- make future changes (e.g. you want percentage rather than ratio) more centralized
- make the intentions of your code much clearer
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