Dear Monks, I am new to perl and still learning the ropes. I am trying to use the foreach loop but not getting the desired output. Here's my code: use warnings; 
print "Please enter the cns file:\n";
chomp($t=<STDIN>);
open(THE,$t) or die "Can not open file: $!\n";
@data=<THE>;
close THE;
$sequence='';
$end=0;
foreach $line(@data){
if($line=~/^\@/){
$chro=$line;
}elsif($line=~/^[a-zA-Z]/){
$sequence.=$line;
}else{
$end++
}
}
$sequence=~s/\s*$//g;

print $chro,"\n";
print $sequence,"\n";

[download]
The file am reading in looks like this: <@chr1 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn @chr2 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn> My problem is this will only output the last iteration i.e @chr2 followed by the nnnn's. How can I make it return the file the way it looks like from the input i.e. @chr1 nnnn.. followed by @chr2 nnn....? thanks.

In reply to foreach loop by morio56

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