[Bioperl-l] question about $feature->add_sub_SeqFeature and Bio::Graphics

June Tantoolvesm june@ics.es.osaka-u.ac.jp
Mon, 6 Jan 2003 12:00:33 +0900


I hope this hasn't already been answered elsewhere. Please accept my
apologies if it has, but I've tried searching and I couldn't find enough

I am using the Bio::Graphics package. All the code from the
Bio::Graphics HOWTO works great (thank you very much), but now I am
trying to modify code example 4, because I am trying to parse an already
parsed blast output.

I am having trouble with the following piece of code, from example 4 of
the HOWTO page:

45    while( my $hsp = $hit->next_hsp ) {
46      $feature->add_sub_SeqFeature($hsp,'EXPAND');
47    }

Is there another way I can add $hsp->query->start, $hsp->query->end,
etc., to the newly-created feature, without calling add_sub_SeqFeature?
Where can I read more about the exact structure of $hsp? Is there a way
I can use straight perl to add my data (not from the original blast
output, but from a parsed blast output) to $hsp?

I tried looking in the module codes themselves but they are too

I hope I'm making some sense. Thank you beforehand for any hints.

Best regards,