I am using Perl for a script that takes in input as two short strings of DNA. As an output, I concatenate the two strings strings then print the second string lined up over its copy at the end of the concatenated string. For example: if input string are AAAA and TTTTT then print:
AAAAATTTTT
TTTTT
I know there are other ways to do this but I am curious to know why my use of tr/// isn't working.
The code for the program is:
use strict;
use warnings;
print "enter a DNA sequence \n";
$DNA1=<>; #<> shorthand for STDIN
$DNA1=~ s/\r?\n?$//;
print $DNA1 "\n\n";
print "enter second DNA sequence \n";
$DNA2=<>;
$DNA2=~ s/\r?\n?$//;
print $DNA2 "\n\n";
$DNA= join("",($DNA1,$DNA2));
print "Both DNA sequences are \"$DNA\" \n\n";
$DNA3=$DNA1;
$DNA3=~ tr/ATCGatcg//;
print $DNA3 "\n\n";
$DNA4= join("",($DNA3,$DNA2));
print $DNA4 "\n\n";
exit;
Your tr changes any of ACTGatcg and removes them. I think you want
$DNA3 =~ tr/atcgATCG/ /;