I cleaned up your code and it now looks as follows:
use strict;
use warnings;

my $filename = 'fasta.txt';

open my $FILE, '<', $filename or die "Could not open $filename: $!";

while(my $line = <$FILE>) {
    if($line=~/^>.*unknown/ ) {
        $line .= <DATA>;
        print $line;
    }
}
close $FILE;

[download]
How do you know your script stopped reading after finding the first header? Are you sure your file contains more than one header?

I ran the above on the following data:

test
not this
> unknown
print this
no no
no again
> known (not this header)
got you!
no way Jose
> HEADER unknown
Yessir!
not this line
throw this away

[download]
Output:
> unknown
print this
> HEADER unknown
Yessir!

[download]

CountZero

A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James

My blog: Imperial Deltronics

In reply to Re: While loop stops after reading new line? by CountZero
in thread While loop stops after reading new line? by JonathanPrice

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