[Bioperl-l] [Bioperl-guts-l] Notification: incoming/1243 (fwd)

[Jason Stajich]

See below

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

---------- Forwarded message ----------
Date: Tue, 10 Sep 2002 17:00:15 -0400
From: bioperl-bugs@bioperl.org
To: bioperl-guts-l@bioperl.org
Subject: [Bioperl-guts-l] Notification: incoming/1243

JitterBug notification

new message incoming/1243

Message summary for PR#1243
	From: fyang68@yahoo.com
	Subject: suggestion about Bio::Search::HSP::HSPI
	Date: Tue, 10 Sep 2002 17:00:13 -0400
	0 replies 	0 followups

====> ORIGINAL MESSAGE FOLLOWS <====

>From fyang68@yahoo.com  Tue Sep 10 17:00:14 2002
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Date: Tue, 10 Sep 2002 17:00:13 -0400
Message-Id: <200209102100.g8AL0DIn025471@pw600a.bioperl.org>
From: fyang68@yahoo.com
To: bioperl-bugs@bioperl.org
Subject: suggestion about Bio::Search::HSP::HSPI

Full_Name: Fan Yang
Module: Bio::Search::HSP::HSPI
Version:
PerlVer:
OS:
Submission from: (NULL) (205.181.102.135)


Hi, bioperl has definitely done great job.  Just
a comment about Bio::Search::HSP::HSPI.  I hope
it can return the positions of HSP of both query
and subject sequences.  For instance:

Query: 213    aaaagtaattgtggtttttgccat 236
              ||||||||||||||||||||||||
Sbjct: 134332 aaaagtaattgtggtttttgccat 134309

I would like to get "213", "236", "134332", from the
object.

Fan:

Here you go -- This is because Bio::Search::HSP::HSPI objects are
Bio::SeqFeature::SimilarityPair objects which contain references to
queries and hits (subjects)

$hsp->query->start    -->     213
$hsp->query->end      -->     236

Start will always be less than end - $hsp->query->strand will give you the
strandedness.  Query strand is 0 for blastp and protein vs DNA db
searches.

$hsp->hit->start     -->     134332
$hsp->hit->end       -->     134309


Thanks.

Fan


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