use strict;
use warnings;

my $in="aphidbase_2.1b_mRNA.fasta";
my $IN;
my $out="141211_Ap_totalmRNA.fasta";
my $OUT;

my $L="";
my $id="";
my $seq="";
my $i=0;


open $IN,"<",$in or die "inerror";
open $OUT,">",$out;

while ($L=<$IN>){
	chomp $L;
	if($L=~ /^>.+/ && $i==0){
		$id= $L;
		print $OUT "$id\n";
		$i=1;
	}
	elsif($L=~ /^>.+/ && $i==1){
	$seq= $L;
	$id= $L;
	print $OUT "\n$id\n";
	}
	else{
	$seq=$L;
	print $OUT "$seq";
	}
}
close $IN;
close $OUT;
exit;