I need to extract from a gbff: 
 gene            complement(<5504..>6553)
                     /locus_tag="OT_ostta02g00030"
                     /old_locus_tag="Ot02g00030"
                     /db_xref="GeneID:9832574"

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the GeneID related to its coordinates $start = 5504 $stop = 6553 There are a lot of genes so I want to make a loop I use Perl for my code, you can see below a part of it (extracting the numbers) but it doesn't work. 
$infile = "GCF.gbff"; 
$outfile = "a1.txt";
open(IN, $infile) or die "Failed to open $infile\n";
open (OUT, ">$outfile") or die "Failed to open $outfile\n";
$n=0;
while ($line = <IN>)  
{  
    chomp ($line); 
    $line =~ s/\r$//;
    if ( $line =~ /<\d+..>\d+/ )
       {     ++$n;   my ($start, $stop) = ($1, $2);
                 print OUT "$start, $stop, $header";
       }
}
print STDERR"$n";                    
sub header
{ 
    @geneID = split /\s+/, $start, $stop; 
    $header = "$fastaprompt$geneID[1]"; 
}
close (IN);
close (OUT);

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In reply to gene location by nica

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