$qual_obj = Bio::SeqIO->new(-file => "/home/Alan/Desktop/sequence_data/$qual_file", -format => "qual"); my %qual_hash = (); while($qual_hash = $qual_obj->_next_qual){ $qual_hash{$qual_obj->id} = $qual_obj->seq; } #### >FQ4HLCS01B2SNT rank=0025082 x=734.0 y=3335.0 length=53 37 37 37 37 37 37 37 37 37 37 37 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 38 38 35 33 32 32 27 27 15 13 13 13 11 14 11 17 17 17 >FQ4HLCS01BGPRG rank=0042480 x=483.0 y=1242.5 length=108 37 37 37 37 37 37 37 37 37 37 37 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 39 39 39 39 39 39 39 39 39 39 39 40 40 37 37 37 37 37 37 35 33 32 27 23 19 17 17 19 19 11 11 11 11 14 22 14 21 25 24 25 25 29 30 30 28 28 28 28 28 28 16 16 11 11 11 11 11 17 16 12 12 17 16 18 17 22 16 12 13 >FQ4HLCS01AY14Q rank=0050917 x=282.0 y=760.0 length=314 29 29 18 14 14 14 14 14 27 30 28 17 19 19 19 31 35 37 30 31 31 37 39 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 39 38 37 37 37 37 37 25 25 21 21 21 21 30 30 35 37 37 35 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 28 28 28 28 37 37 37 37 30 30 23 23 23 32 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 35 35 35 35 33 32 28 18 18 21 21 25 25 28 33 33 33 32 32 32 33 33 33 30 25 25 21 21 21 25 25 32 32 35 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 38 37 35 35 33 33 33 16 16 17 17 17 27 11 19 19 22 21 21 23 23 23 23 23 24 23 19 23 27 27 19 19 19 23 23 28 27 27 27 27 17 17 19 24 23 21 21 11 11 11 22 22 24 16 12 11 11 0 12 12