my %id2seq = (); my $id = ''; open File,"human_hg19_circRNAs_putative_spliced_sequence.fa",or die $!; while(){ chomp; if($_ =~ /^>(.+)/){ $id = $1; }else{ $id2seq{$id} .= $_; } } my $filename = "'$id'"; open (my $fh, '>', $filename) or die "Could not open '$filename' $!"; foreach $id (keys %id2seq){ print $fh ($id."\n",$id2seq{$id}, "\n"); } close File; close $fh;