Question

I have this snippet;

print "$score\n";
for (my $i = 0; $i < $n; $i++)
{
print $output[$i];
if($i == $center)
{
    print "*";
}
print "\n";
}

and it should print this:

-62
ttagggcccgg-a-tc---attaccgggc--caa
tta--gcgcgg-attcg-gatta-cggg---c-a*
gcg--gggcggcattagcaattt-gggg-atc-a
-ta--gcgc---a-----aataa-ccgg------

but instead it prints this:

-62
ttagggcccgg-a-tc---attaccgggc--caa
*ta--gcgcgg-attcg-gatta-cggg---c-a
gcg--gggcggcattagcaattt-gggg-atc-a
-ta--gcgc---a-----aataa-ccgg------

If i remove the “*”, the strings are correct (they are really the strings i want to print), the problem is its placing. this is printed:

-62
ttagggcccgg-a-tc---attaccgggc--caa
tta--gcgcgg-attcg-gatta-cggg---c-a
gcg--gggcggcattagcaattt-gggg-atc-a
-ta--gcgc---a-----aataa-ccgg------

Why is it printing on the beginning of the string, and not on te end as it is supposed to?

Thanks a lot.

Answer 1

Your code works perfectly on a *nix system where \n is the only line terminator and the lines of text in @output do not end in \n.

#!/usr/bin/perl

my @output = ("ttagggcccgg-a-tc---attaccgggc--caa",
              "tta--gcgcgg-attcg-gatta-cggg---c-a",
              "gcg--gggcggcattagcaattt-gggg-atc-a",
              "-ta--gcgc---a-----aataa-ccgg------");

my $center = 1;
my $score = -62;

print "$score\n";
for (my $i = 0; $i < 4; $i++)
{
    print $output[$i];
    if($i == $center)
    {
        print "*";
    }
    print "\n";
}

Output:

-62
ttagggcccgg-a-tc---attaccgggc--caa
tta--gcgcgg-attcg-gatta-cggg---c-a*
gcg--gggcggcattagcaattt-gggg-atc-a
-ta--gcgc---a-----aataa-ccgg------

The only way I see your code generating the output you post is if each line of text contained in @output ends with a \r which would cause the carriage return to occur, then you’d print the * (which would overwrite the first character of the line you just output) followed by the \n at the bottom of your loop.

If I change @output in my example to:

my @output = ("ttagggcccgg-a-tc---attaccgggc--caa\r",
              "tta--gcgcgg-attcg-gatta-cggg---c-a\r",
              "gcg--gggcggcattagcaattt-gggg-atc-a\r",
              "-ta--gcgc---a-----aataa-ccgg------\r");

Then the output is:

-62
ttagggcccgg-a-tc---attaccgggc--caa
*ta--gcgcgg-attcg-gatta-cggg---c-a
gcg--gggcggcattagcaattt-gggg-atc-a
-ta--gcgc---a-----aataa-ccgg------

SO the final answer is: Get rid of the \r at the end of those. 🙂

Edit: As TLP points out in the comments below, using a regex substitution to make sure that there’s nothing on the end of those lines should fix you up:

for (my $i = 0; $i < 4; $i++)
{
    $output[$i] =~ s/\s*$//;
    print $output[$i];
    ...

Last Edit: From the comments below from TLP, I would guess this data is read from a file that came from a windows machine where lines end in \r\n. When reading that file in perl on OSX, you’re using chomp to remove newlines. In OSX, chomp is only going to remove \n (by default) and leave the \r intact.