[Bioperl-l] Hit length using length_aln()

[Jason Stajich]

I have a SearchIO HOWTO started that is in CVS (doc/howto) which is where
I'd like to see this stuff accumulate.  See my next post.

-j

On Mon, 15 Jul 2002, Wiepert, Mathieu wrote:

> Thanks for the debug tips, those are really useful, and perhaps worth
> a comment somewhere in the documentation?  I know it's not bioperl
> related really, but tips/tricks for the bioperl programmer are always
> nice.
>
> -Mat
>
> -----Original Message-----
> From: Brian Desany [mailto:bdesany@bcm.tmc.edu]
> Sent: Friday, July 12, 2002 6:16 PM
> To: 'Ken'; bioperl-l@bioperl.org
> Subject: RE: [Bioperl-l] Hit length using length_aln()
>
>
> Ken,
>
> I just saw Jason's post, but here's my input anyway:
>
> To find the length of the query, the subject (a.k.a. hit) and the hsp:
>
> $result->query_length
> This is a Bio::Search::Result::GenericResult (gets all it's methods from
> Bio::Search::Result::ResultI I think).
>
> $hit->length
> This is a Bio::Search::Hit::GenericHit, which doesn't have a length_aln
> method.
>
> $hsp->length
> This is a Bio::Search::HSP::GenericHSP
>
> When I run into issues like this I like to go into the perl debugger and
> type 'm $object' to see what methods the object has, and as a bonus it tells
> you from where in it's inheritance it get it. To see what kind of object you
> have in the first place, type 'x ref($hsp)'. This has been really useful to
> me in figuring out a lot of bioperl (incl. the Blast parsing parts) because
> it can be kinda complicated.
>
> HTH
>
> -Brian.
>
>
>
> >-----Original Message-----
> >From: bioperl-l-admin@bioperl.org
> >[mailto:bioperl-l-admin@bioperl.org]On
> >Behalf Of Ken
> >Sent: Friday, July 12, 2002 5:55 PM
> >To: bioperl-l@bioperl.org
> >Subject: [Bioperl-l] Hit length using length_aln()
> >
> >
> >I'm still learning BioPerl so bear with me.
> >I want the total length for a hit across all the HSPs so I
> >figured I should
> >use length_aln.
> >All I get is an error message:
> >  Can't locate object method "length_aln" via package
> >"Bio::Search::Hit::GenericHit"
> >
> >I can't locate length_aln() in that package either, so Perl
> >and I agree
> >there...
> >I found it in Bio::Search::Hit::BLASTHit.
> >
> >I'm able to return all of the HSPs from the hit object - so I
> >know that I've
> >got a good reference to the hit.
> >
> >The code is pretty straightforward:
> >---------------------------------------------------------------
> >--------------------------
> >my $searchio = new Bio::SearchIO ('-format' => 'blast', '-file'
> >=>$blastfile );
> >my $result = $searchio->next_result;
> ># get info about the first hit
> >while( my $hit = $result->next_hit()) {
> >	my @hsps_lens;
> >	my $hit_name = $hit->name ;
> >	#for each hit look at each HSP
> >	my @hsp_s = $hit->hsps();
> >	my $lenObj = $hit->length_aln();
> >---------------------------------------------------------------
> >--------------------------
> >If I remove the reference to length_aln() everything works.
> >I've thought about creating something that adds the length of
> >each HSP, but I
> >figured that's what length_aln() does.
> >Any ideas why this doesn't work?
> >Thanks in advance for any help,
> >Ken Graham
> >Biological Chemistry
> >U.C. Davis School of Medicine
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l@bioperl.org
> >http://bioperl.org/mailman/listinfo/bioperl-l
> >
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu