[Bioperl-l] Generate a hsp from emboss format?

[Fields, Christopher J]

On Mar 18, 2013, at 7:00 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Mon, Mar 18, 2013 at 11:43 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>> 
>> Hi,
>> I have a script who uses emboss (water) for a dynamic programming alignment.
>> Is this possible to generate (convert) my result in emboss format in a hsp
>> (blast) like.
>> 
>> I need (I think) an hsp format because it's much easier for parse only one
>> of the two strand in the alignment (and this is what I need).
>> 
>> Thanks!
> 
> EMBOSS water (and related tools like needle) support a range of output
> formats - have you looked at those yet?
> 
> Peter


Antony,

Bio::AlignIO::emboss is supposed to support water/needle output; have you tried that?  Also, I'm not sure what advantage having this in a BLAST-like output would have over other human-readable formats; any reasons you would need this specific output?

chris