How can I input the "input_file"? "$input_file" is a scalar but not a file. I run the following script:

#!/usr/local/bin/perl
use warnings;
open ( my $input_fh, "<", $genome );
open ( my $output_fh, ">", $output_file );
foreach my $line ( <$input_fh> )
{
  unless ( $line =~ m/\A\s*\Z/ )
  {
    $line =~ s/(GL\d{6})\d+/$1/;
    print $output_fh $line;
  }
}
close ( $input_fh );
close ( $output_fh );

[download]
and got the following messages:

Name "main::genome" used only once: possible typo at header.pl line 3. Name "main::output_file" used only once: possible typo at header.pl line 4. Use of uninitialized value $genome in open at header.pl line 3. Use of uninitialized value $output_file in open at header.pl line 4. readline() on closed filehandle $input_fh at header.pl line 5.

I think my way to open the file is wrong. Can you give me some hints? Thanks XF

In reply to Re^2: Shorten the headers of a file and remove empty lines using perl by Anonymous Monk
in thread Shorten the headers of a file and remove empty lines using perl by intect

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