[Bioperl-l] needle parser in bioperl?

[Chris Fields]

On Dec 12, 2006, at 6:14 AM, neeti somaiya wrote:

> Hi,
>
> Does anyone know of a bioperl parser for needle output, basically I  
> won't
> where the target sequence aligns on the template (i.e. coordinate  
> on the
> template where the taget aligns).
>
> -- 
> -Neeti
> Even my blood says, B positive

I answered this a number of months back:

http://tinyurl.com/yzlbx5

Basically, newer versions of EMBOSS have changed the output for the  
AlignIO::emboss parser (which parses needle).  I don't believe the  
parser has been fixed to deal with that, but Jason has pointed out  
you can use MSF output when running needle, then parse using AlignIO  
with the format set to 'msf'.

chris