[EMBOSS] Reading Two Sequences from stdin with water

[simon andrews (BI)]

On 3 Jun 2005, at 16:23, andrew warry ((BITS)) wrote:

>
>> Is there a solution to this? I would really like to avoid the mess of
>> temporary files and run water in a clean pipe (pun intended  ;-)  )
>
> Hi
> How about :
>
> nthseq x.fasta -number 2 -stdout -auto | water -aseq stdin -bseq 
> x.fasta
> -stdout -auto
>
> It isn't very neat and does a redundant comparison but it does the job!

But x.fasta still has to appear on the filesystem.  You can't run this 
cleanly in a pipe.

Simon.