[Bioperl-l] StandAloneBlast

Sendu Bala bix at sendu.me.uk
Thu Jun 19 10:32:05 EDT 2008


byuhobbes wrote:
> I'm running blastall with StandAloneBlast for the first time.  There is quite
> a bit of documentation about how to run the blast, and how to get your blast
> report object, but I am having trouble finding documentation on what values
> you can retrieve from the report object and how you do so.

Look at the documentation for the objects you retrieve.

http://docs.bioperl.org/bioperl-live/Bio/SearchIO/blast.html

$searchio->next_result returns a Bio::Search::Result::ResultI, actually 
a Bio::Search::Result::BlastResult:

http://docs.bioperl.org/bioperl-live/Bio/Search/Result/BlastResult.html
which isa:
http://docs.bioperl.org/bioperl-live/Bio/Search/Result/GenericResult.html

These return $hit = $result->next_hit() Bio::Search::Hit::HitI objects:

http://docs.bioperl.org/bioperl-live/Bio/Search/Hit/BlastHit.html
http://docs.bioperl.org/bioperl-live/Bio/Search/Hit/GenericHit.html

which in turn will give you HSP objects:

http://docs.bioperl.org/bioperl-live/Bio/Search/HSP/BlastHSP.html
http://docs.bioperl.org/bioperl-live/Bio/Search/HSP/GenericHSP.html




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