[Bioperl-l] a problem with HspI module?

[Dimitar Kenanov]

Hello guys,
i think i found a problem with ' Bio::Search::HSP::HSPI'. Consider the 
following HSP:
-------------
Score = 48.9 bits (115),  Expect = 8e-04, Method: Compositional matrix 
adjust.
  Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 14/77 (18%)
  Frame = +1

Query  371      
PSGMLLA-----SCSDDMTLKIWSMKQEVCIHDLQAHNKEIYTIKWSPTGPATSNPNSNI  425
                 P   LLA     S S D T+++W ++Q VC H L  H + +Y++ +SP G
Sbjct  6955270  
PGLQLLAFSHPPSASFDSTVRLWDVEQGVCTHTLMKHQEPVYSVAFSPDGK---------  6955422

Query  426      MLASASFDSTVRLWDIE  442
                  LAS SFD  V +W+ +
Sbjct  6955423  YLASGSFDKYVHIWNTQ  6955473
---------------

The method 'frac_identical' is not functioning right.
-------------
Title   : frac_identical
  Usage   : my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] );
  Function: Returns the fraction of identitical positions for this HSP
  Returns : Float in range 0.0 -> 1.0
  Args    : 'query' = num identical / length of query seq (without gaps)
            'hit'   = num identical / length of hit seq (without gaps)
            'total' = num identical / length of alignment (with gaps)
            default = 'total'
---------------
According to the method description, for the HSP above, 'frac_identical' 
should return '0.42' with 'hit'. But it doesnt. Now with 'hit' gives 
'0.13'. With 'total' gives normal result '0.35'.

Thats all.
Cheers

Dimitar

-- 
Dimitar Kenanov
Postdoctoral research fellow
Protein Sequence Analysis Group
Bioinformatics Institute
A*STAR, Singapore
tel: +65 6478 8514