cburger has asked for the wisdom of the Perl Monks concerning the following question:

I'm trying to write a script which replaces one letter with another for nucleotide bases. e.g. A with T. when I write:

for example I want to convert this string:

AAGCTT

with:

TTCGAA

I wrote something like:

while(/(.)/g) {
my $letter= uc $1;
print $letter;
my $len=length($letter);

my $sub="";
if ($letter=="A") { $sub="T";}
elsif ($letter=="T") { $sub="A";}
elsif ($letter=="G") { $sub="C";}
elsif ($letter=="C") { $sub="G";}
print "  $len\t$sub\n"; 
} # close while

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the replacement is not correct and I get for the print out:

A  1    T
A  1    T
G  1    T
C  1    T
T  1    T
T  1    T

[download]

what is happening? why is sub always T and not changing? I dont see the problem with the lines.. thanks for the help!

thanks everyone! I could figure out the problem now. Indeed the eq sign mix up was the problem, and I wasnt aware of the tr// possibility. Painful learning from sloppiness...Thanks again for the help perlmonks!

Replies are listed 'Best First'.
Re: problems with converting a string character by character
by toolic (Bishop) on Feb 02, 2011 at 01:02 UTC
    If you use strict and warnings, you will see these warnings: 
    Argument "A" isn't numeric in numeric eq (==)

    [download]
    You need to use string equality. Change == to eq 
    use warnings;
use strict;

$_ = 'AAGCTT';
while (/(.)/g) {
    my $letter = uc $1;
    print $letter;
    my $len = length($letter);

    my $sub = "";
    if    ( $letter eq "A" ) { $sub = "T"; }
    elsif ( $letter eq "T" ) { $sub = "A"; }
    elsif ( $letter eq "G" ) { $sub = "C"; }
    elsif ( $letter eq "C" ) { $sub = "G"; }
    print "  $len\t$sub\n";
}    # close while

__END__

A  1    T
A  1    T
G  1    C
C  1    G
T  1    A
T  1    A

    [download]
    Another way to do it is with a hash: 
    my %conv = (
    A => 'T',
    T => 'A',
    G => 'C',
    C => 'G',
);

$_ = 'AAGCTT';
while (/(.)/g) {
    my $letter = uc $1;
    print $letter;
    my $len = length($letter);
    print "  $len\t$conv{$letter}\n";
}

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Re: problems with converting a string character by character
by Anonyrnous Monk (Hermit) on Feb 02, 2011 at 00:59 UTC

    Use eq in place of ==.

    But maybe you're rather looking for tr/ATGC/TACG/.  See tr.

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Re: problems with converting a string character by character
by jethro (Monsignor) on Feb 02, 2011 at 01:09 UTC

    By the way, there is already a builtin function for this. Your script could be written as

    $_= uc($_);
tr/ATGC/TACG/;

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