[Bioperl-l] HSP length/percent identity bug?

[Lu, Hong]

I am using Bio::SearchIO to parse wu-blastn report. I found there is a bug
in the module for 
$hsp->length and $hsp->percent_identity that broke my script: 

Example:

HSP:

subject:   2051    TA-CGATGCTC      2060
                         TA CG    GCTC
                9        TATCG--GCTC     1
                  
The above wu blastn object, $hsp->length = 10 ,  $hsp->percent_identity  =
80 %.

Obviously, the correct answer should be:
      $hsp->length = 11 ,  $hsp->percent_identity  = 3/11 =  72.7 %.

Is the above bug known?


Hong (Henry) Lu
Bioinformatics Scientist
454 Corporation
Branford, CT 06405