[Bioperl-l] Bio::SearchIO TFASTX parsing bug

Aaron J. Mackey amackey at pcbi.upenn.edu
Mon Oct 25 20:11:13 EDT 2004

Fixed, thanks for the report.  Your daily CVS update should get the 
patch soon.


Daniel Mascarenhas wrote:

> Hello,
> we've been using $hit->logical_length('query') on TFASTX reports and 
> noticed that it corresponds to $result->query_length divided by 3. That 
> is exactly what we would expect  for TBLASTX, where both the query and 
> hit sequences are translated into aminoacid sequences, however, TFASTX 
> compares a protein sequence to a DNA sequence database and therefore 
> just the hit logical length makes sense. So, everything else that 
> depends on the $hit->logical_length('query') is miscalculated.
> We're using bioperl-live from cvs (updated almost daily).
> Cheers,
> Daniel
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