my %id2seq = (); my $id = ''; open File,"human_hg19_circRNAs_putative_spliced_sequence.fa",or die $!; while(){ chomp; if($_ =~ /^>(.+)/){ $id = $1; }else{ $id2seq{$id} .= $_; } } foreach $id (keys %id2seq){ open my $out_fh, '>>', $id or die $!; ##Amendment here print $out_fh ($id."\n",$id2seq{$id}, "\n"); close $out_fh; ## moved into the foreach loop } close File;