[Bioperl-l] Getting 'features' from SearchIO?

Dan Bolser dan.bolser at gmail.com
Mon May 11 10:34:22 EDT 2009


I am parsing a blasttable and extracting Bio::Search::HSP::GenericHSP
objects as a result. I read somewhere that HSP objects inherit Feature
objects... How can I get a 'standard' representation of the HSP as a
feature? Basically I'd like to simply load the blast results into a
feature database...

When I call feature methods on the HSP objects I just get blank or
undef results... I think this is because I'm trying to get at the
sequences existing (non existent) features, rather than get the HSP
object as a feature... If that makes sense... How can I confirm that I
have a feature object containing the details of the HSP?

I thought of trying to just pass the HSP object to the
Bio::DB::SeqFeature::Store, but I need to get that up and running
first (I'm looking into it). In the mean time I thought I'd ask if
this sounds like the right thing to do.

More generally I want to have features attached to sequences that are
themselves annotations of larger sequences (but with unknown
position). Is Bio::DB::SeqFeature::Store a way to go? I need to manage
various different bits of information coming from a sequencing
project, and I need a solution to the whole 'assembly life cycle
management' problem.

Thanks for any help,

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