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Reading in Qual File Using Bio::SeqIO

by twaddlac (Novice)
on Jul 01, 2010 at 19:22 UTC ( #847595=perlquestion: print w/ replies, xml ) Need Help??

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  1. or download this
    $qual_obj = Bio::SeqIO->new(-file => "/home/Alan/Desktop/sequence_data
    +/$qual_file", -format => "qual");
    
    ...
    while($qual_hash = $qual_obj->_next_qual){
         $qual_hash{$qual_obj->id} = $qual_obj->seq;
    }
    
  2. or download this
    >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 4
    +0 40 40 40 40 40 40 40 40 40 40 40 38 38 35 33 32 32 27 27 15 13 13 1
    +3 11 14 11 17 17 17 
    ...
    37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 3
    +7 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 3
    +7 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 1
    +7 17 17 27 11 19 19 22 21 21 23 23 23 23 23 24 23 19 23 27 27 19 19 1
    +9 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 
    

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