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;