Why isn't Perl's tr/// doing what I want?

Question

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;

Is this just poorly formatted or is Perl's syntax format actually look like this? — Bobby Cannon, Apr 28 '09 at 15:25
yes "$DNA1=~ s/\r?\n?$//;" is the same as "chomp $DNA. but perl 4 and lower versions dont support chomp so its an alternative. and my machine has perl 4 installed. — shubster, Apr 28 '09 at 15:31
@Alnitak & @Bobby - and, assuming perl 4 on the target machine, the code can't look much better (those stricts and warnings are not going to do much either). Aside: it's truly scary to find a machine running perl 4. Perl 5 was released fifteen years ago! — Nic Gibson, Apr 28 '09 at 16:00
$DNA1=~ s/\r?\n?$//; is only the same thing as chomp if the input record separator is \r\n, which it might not be. — brian d foy, Apr 29 '09 at 15:02

score 1 · Answer 1 · answered Apr 28 '09 at 15:27

1

You need to put a space in the second half of the tr command.

Alternatively, it seems that what you're trying to do is create a variable containing as many spaces as there were characters in the first string:

my $spaces = ' ' x length($DNA1);

answered Apr 28 '09 at 15:27

Alnitak

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score 1 · Accepted Answer · answered Apr 28 '09 at 15:27

1

Your tr changes any of ACTGatcg and removes them. I think you want

$DNA3 =~ tr/atcgATCG/ /;

answered Apr 28 '09 at 15:27

Paul Tomblin

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not nothing, it counts them (but the returned count is unused here) – ysth Apr 29 '09 at 04:25

score 1 · Answer 3 · answered Apr 28 '09 at 15:29

It might just be a simple syntax error. Try:

$DNA3 =~ tr/ATCGatcg/ /;

where the second slash separates your two translation entities, and you have a space character between the second and third slashes.

Good luck!

Edit: my mistake - misunderstood what you wanted to do. Answer adjusted accordingly :)

score 0 · Answer 4 · answered Apr 29 '09 at 15:00

0

Is this the program that you want?

#!perl

my $s1 = 'AAAAAAAAA';
my $s2 = 'TCGAGCTA';

print 
    $s1, $s2, "\n", 
    ' ' x length( $s1 ), $s2, "\n";

answered Apr 29 '09 at 15:00

brian d foy

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Why isn't Perl's tr/// doing what I want?

4 Answers4