[Bioperl-l] Parsing needle/water output

[Kevin Brown]

http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3
A%3AAlignIO%3A%3Aemboss&sort_order=by+method&search_string=Bio%3A%3AAlig
nio%3A%3Aemboss 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> shalabh sharma
> Sent: Thursday, May 14, 2009 1:14 PM
> To: Scott Markel
> Cc: bioperl-l
> Subject: Re: [Bioperl-l] Parsing needle/water output
> 
> yes, i tried to read the documentation about 
> Bio::AlignIO::emboss, but there
> is not much in it.So is like i can call the same functions 
> which are used in
> searchIO. I need start and end position of the pairwise alignment.
> 
> Thanks
> Shalabh
> 
> 
> On Thu, May 14, 2009 at 3:58 PM, Scott Markel 
> <SMarkel at accelrys.com> wrote:
> 
> > Shalabh,
> >
> > Have you looked at Bio::AlignIO::emboss?
> >
> > Scott
> >
> > Scott Markel, Ph.D.
> > Principal Bioinformatics Architect  email:  smarkel at accelrys.com
> > Accelrys (SciTegic R&D)             mobile: +1 858 205 3653
> > 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
> > San Diego, CA 92121                 fax:    +1 858 799 5222
> > USA                                 web:    http://www.accelrys.com
> >
> > http://www.linkedin.com/in/smarkel
> > Vice President, Board of Directors:
> >    International Society for Computational Biology
> > Co-chair: ISCB Publications Committee
> > Associate Editor: PLoS Computational Biology
> > Editorial Board: Briefings in Bioinformatics
> >
> >
> > > -----Original Message-----
> > > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > > bounces at lists.open-bio.org] On Behalf Of shalabh sharma
> > > Sent: Thursday, 14 May 2009 12:54 PM
> > > To: bioperl-l
> > > Subject: [Bioperl-l] Parsing needle/water output
> > >
> > > Hi All,
> > >          Is there any parser/module available to parse 
> needle/water
> > output
> > > report (from emboss) to get the start and end position of 
> alignment.
> > >
> > > Thanks
> > > Shalabh
> > > _______________________________________________
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> > > Bioperl-l at lists.open-bio.org
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> >
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