use strict; use warnings; use Bio::SeqIO::qual; my $file = "Qual.txt"; my $qual_obj = Bio::SeqIO::qual->new(-file =>"<$file",-format=>'qual',); my %qual_hash ; while(my $qual = $qual_obj->_next_qual){ $qual_hash{$qual->id}= $qual->qual(); } use Data::Dumper; print Dumper(\%qual_hash);