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