[EMBOSS] eprimer32 question

[Peter Cock]

On Mon, Aug 27, 2012 at 11:16 AM, Ivaylo Stoimenov
<ivaylo.stoimenov at gmail.com> wrote:
> Hi Peter and Peter,
> Many thanks to both of you for the valuable help. It is very important for
> me to have as less file-related operations as possible, and passing a
> string helps to reduce the input from files.
> I wondered if it is possible to hijack the output of Primer3 to some sort
> of object directly to eprimer32 without writing to a file and thus making
> Primer3 sort of a function to an external program. I am aiming of running a
> validation cycle for the primers suggested by Primer3 and if necessary to
> change the input to Primer3 until certain criteria are fulfilled. Therefore
> I would like to skip a file-write-read operation until everything is
> optimal. Do you know if that is still possible, or I always need to read
> from Primer3 output files.

I think what you're asking for would require compiling the EMBOSS
or underlying Primer3 function into your program. That may not be
possible due to licensing restrictions (e.g. EMBOSS is GPL, what
does your tool use?).

However, you should be able to avoid a file-write-read by asking
EMBOSS to write the output to stdout, and reading that from your
program.

(This is related to the other suggestion I made for passing the
sequence to EMBOSS without using an input file: You can do
this in the command line using the "asis" trick, or use stdin.)

Peter