[Bioperl-l] Blastx parser misses scores

[Jason Stajich]

Can you please provide and example report and code which doesn't behave as
you would expect.

Are you talking about the case where you have 50 hits listed in the
summary but say only 25 HSP alignments?


On Fri, 5 Sep 2003, Holland, Richard wrote:

> 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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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu