[EMBOSS] is it possible to use emboss without writing a full application?

Peter Rice ricepeterm at yahoo.co.uk
Fri Apr 4 19:27:02 UTC 2014

On 04/04/14 14:30, Daily, Jeff A wrote:
 > EMBOSS Community,
 > I’ve looked at the example application “seqret” and I think I 
understand it well enough.  However, I am more interested in being able 
to programmatically call the “needle” application without a system call. 
  More specifically, I would like to simply use emboss’s NW alignment 
function *without* writing a full application.  I guess another way to 
ask this is, I have a completely different way of gathering command-line 
user input that doesn’t use Ajax/ACD, can I still use emboss for 
sequence alignment?  That’s the kind of example I need.  Any help is 
appreciated.  Thanks.

Yes, you can create sequences and other datatypes from a string (which 
is basically what ACD does internally) and simply call the setup 
functions if you need, for example, the EMBOSS database handling enabled.

You will find the functions you need in ajax/acd/ajacd.c

Let us know if you need any further help. Maybe some of the functions do 
not work ideally in a standalone mode - we have not tried them that way 
since the early versions but, by design, it should be straightforward to do.


Peter Rice

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