[EMBOSS] Reading Two Sequences from stdin with water

[simon andrews (BI)]

On 3 Jun 2005, at 13:53, Jan T. Kim wrote:

> Dear EMBOSSers,
>
> is it possible to read both input sequences to a pairwise alignment
> from one input stream?

I spent a while trying to figure this out a few months back.  In the 
end the best solution I came up with was to use the asis: sequence 
type.  This allows you to do:

water -auto asis:aaaa asis:ataa stdout

which avoids the need for messing with the file system.  I seem to 
remember I found a way to set names for the sequences as well, but 
can't find that right now.

As long as you make sure you don't pass your command through a shell 
when you launch this from a script then it actually scales pretty well 
to quite large sequences.

Hope this helps

Simon.
-- 
Simon Andrews PhD
Bioinformatics Dept.
The Babraham Institute

simon.andrews at bbsrc.ac.uk
+44 (0) 1223 496463