While loop stops after reading new line?

[JonathanPrice]

hello I am having a bit of an issue (i am new to perl) i have written a script that is supposed to read a FASTA file hopefully this will scroll through the file search for ">" and header (it does this). then save this line and the next line in two separate scalars. but it stops after reading the next line? does anyone know why this is? or how i can make it so that it carries on reading the file after finding the 1st correct sequence?? this is my code. thank you.

use strict;
use warnings;


my($filename) = "fasta.txt";

open(FILE, $filename);

while(<FILE>)
{
   my($line) =$_;
   if($line=~/^>/ and $line =~ /unknown/ )
   {
       my($header) =$line; 
       print $header;                             
       <FILE>;
       print $_; 

     }   
 }  
            
 close FILE;
 exit;

[CountZero]

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;

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

Output:

> unknown
print this
> HEADER unknown
Yessir!

[toolic]

Maybe you want:

        $_ = <FILE>;

• Post a few lines of your input file (less than 10 lines which demonstrate your problem).
• Post your actual output.
• Post your expected output.

[Marshall]

For FASTA file format see: http://en.wikipedia.org/wiki/FASTA_format#Format

I would suggest a Perl module at: http://www.bioperl.org/wiki/Main_Page