[Bioperl-l] (no subject)

Sendu Bala bix at sendu.me.uk
Tue Jul 22 11:05:03 EDT 2008

Dhr. R. de Jonge wrote:
> Hi all,
> Thanks for the very quick responses. I've been trying to fix it today,
> trying both the bl2seq method and the direct approach. Unfortunately,
> I'm unable to fix either of the two.
> At the moment I'm trying to get the direct approach working, however,
> I'm not able to obtain the hit_start and hit_end numbers of the
> domain. It seems that these methods, which are not implemented in the
> Bio::Search::HSP::HMMERHSP module (which I used to obtain the domain
> sequence). I've screened through the appropriate modules, with no
> luck. Is there a method to obtain these hit_start/hit_end figures by
> parsing?

The methods are called start() and end().
If $hsp->start doesn't work, try $hsp->hit->start & $hsp->query->start 
instead. If that's the wrong answer, try using the 'hmmer_pull' parser 
and $hsp->start('query') & $hsp->start('hit'). (likewise for end())

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