[Bioperl-l] Blastx parser misses scores

[Holland, Richard]

Hi,

I have run into a problem with Bio::SearchIO::blast parsing blastx
result files. This may affect other blast outputs as well but I'm not
sure.

At the top of a blastx output there is a summary of the best hits in the
results file. Then, all the hits are listed, even the ones which are not
in the best hits list.

The Bio::Perl parser successfully parses all the hits from the file,
however it only returns scores for those which appear in the summary. I
have found the code which does this in Bio::SearchIO::blast and noticed
that this seems to be deliberate - in all cases, blastx or not, the
scores are taken from the summary, and the scores in the hit details
appear to be ignored.

Is this a feature or a bug? We would like to be able to use Bio::Perl to
parse out all the results from our blast reports including all their
scores and details, regardless of whether or not they appear in the best
hits summary.

Can anyone help?

cheers,
Richard
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