[EMBOSS] Reading Two Sequences from stdin with water

[simon andrews (BI)]

On 3 Jun 2005, at 16:40, Jan T. Kim wrote:

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

The only limit is imposed when the command is passed through a shell, 
and is then dependent on the shell you're using.  If you can call the 
program without going through a shell then there should be no limit 
(beyond normal OS memory limits).

The method for doing this varies with the language you're writing the 
script in, but for example in Perl:

system ("water -auto asis:gatc asis:gatc stdout")

would pass the arguments through a shell, whereas

system("water", "-auto", "asis:gatc","asis:gatc","stdout")

would not.

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

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