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

[download]

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!

In reply to problems with converting a string character by character by cburger

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