[Bioperl-l] Re: [Bioperl-guts-l] Notification: incoming/1037

[Jason Eric Stajich]

Fernan -
This is the inteneded behavior - the strand is changed to -1 when start
comes after end in a hit.

-jason

On Fri, 23 Nov 2001 bioperl-bugs@bioperl.org wrote:

> JitterBug notification
>
> new message incoming/1037
>
> Message summary for PR#1037
> 	From: fernan@iib.unsam.edu.ar
> 	Subject: BPlite: are sbjct->start and sbjct->end switched?
> 	Date: Fri, 23 Nov 2001 14:04:02 -0500
> 	0 replies 	0 followups
>
> ====> ORIGINAL MESSAGE FOLLOWS <====
>
> >From fernan@iib.unsam.edu.ar Fri Nov 23 14:04:02 2001
> Received: from localhost (localhost [127.0.0.1])
> 	by pw600a.bioperl.org (8.11.2/8.11.2) with ESMTP id fANJ42A17809
> 	for <bioperl-bugs@pw600a.bioperl.org>; Fri, 23 Nov 2001 14:04:02 -0500
> Date: Fri, 23 Nov 2001 14:04:02 -0500
> Message-Id: <200111231904.fANJ42A17809@pw600a.bioperl.org>
> From: fernan@iib.unsam.edu.ar
> To: bioperl-bugs@bioperl.org
> Subject: BPlite: are sbjct->start and sbjct->end switched?
>
> Full_Name: Fernan Aguero
> Module: BPlite
> Version: 0.7.2
> PerlVer: 5.6.1
> OS: FreeBSD-4.3
> Submission from: (NULL) (200.3.113.15)
>
>
> When parsing a Plus/Minus HSP in a BLASTN report I always get the subject start
> < subject end, which is not the case (should be the opposite).
>
> My code:
> $qs = $hsp->query->start;
> $qe = $hsp->query->end;
> $ss = $hsp->subject->start;
> $se = $hsp->subject->end;
>
> The HSPs (taken from the BLAST output):
> Query: 33      ...[atcg]... 92
>                ... |||| ...
> Sbjct: 9659632 ...[atcg]... 9659573
>
> Query: 93      ...[atcg]... 152
>                    ||||
> Sbjct: 9659572 ...[atcg]... 9659513
>
>
> Query: 153     ...[actg]... 177
>                    ||||
> Sbjct: 9659512 ...[actg]... 9659488
>
> Now 'print $qs $qe $ss $se' produces the following:
>
> QS  QE    SS      SE
> 33  92    9659573 9659632
> 93  152 | 9659513 9659572
> 153 177 | 9659488 9659512
>         +----------------->wrong!
>
> The problem is that BPlite does not provide (or at least I can't find it in the
> docs) something like $hsp->strand. So I need to do a check on 'start > end' to
> see if the result is t or f and then decide on the strand.
>
>
>
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>

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