[EMBOSS] Reading Two Sequences from stdin with water

[Jan T. Kim]

On Fri, Jun 03, 2005 at 01:16:58PM +0100, simon andrews wrote:
> 
> 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.

That's a good idea which I hadn't thought of. Thanks for that. I don't
need any names, other than for purposes of identifying the sequence
within a multisequence file, which is not necessary with this solution.

> 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.

Hmm... isn't there any OS specific limitation to the length of arguments?
But anyway, this is not an issue for me in my case, where sequence
length does not exceed a few hundred symbols.

Best regards, Jan
-- 
 +- Jan T. Kim -------------------------------------------------------+
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