while ($file=){ chomp $line; if($file =~/^[a-z](.*?)(?=(\z))/msg){ $seq=$1; $seq=~ s/\n//; push @seqs, $seq; print OUTFILE2 @seqs; exit; } elsif($file =~/*/){ $header =$fastafile; chomp $header; $header=~s/>//; push @headers, $header; print OUTFILE "$header\n"; }