# this may help
    while (my $line = <FILE>) {

       # The entire line with a substitution
       # if( $line =~ s/^>\S+\/>contig_$count) { 
 
       # Substitution and 1st contiguous sequence         
       if( $line =~ s/^>\S+\s+(\S+)/>contig_$count $1\n/) {
	   print OFILE $line;
           $count++;
       }
   }
   close FILE;
   close OFILE;