[EMBOSS] eprimer32 question

Ivaylo Stoimenov ivaylo.stoimenov at gmail.com
Mon Aug 27 10:16:41 UTC 2012

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.

Kind regards,

2012/8/24 Peter Rice <ricepeterm at yahoo.co.uk>

> Dear Ivaylo and Peter,
> On 24/08/2012 15:59, Peter Cock wrote:
>> On Fri, Aug 24, 2012 at 3:46 PM, Ivaylo Stoimenov
>> <ivaylo.stoimenov at gmail.com> wrote:
>>> Hi,
>>> I was wondering if it is possible for eprimer32 to read a sequence from a
>>> string. The default input is from a file, but I need to feed primer3
>>> from a
>>> string, which is changing in the body of my program. Any help will be
>>> appreciated.
>>>  Many EMBOSS tools will take a sequence on the command line
>> using the pretend file format "asis" (as is), or can read from stdin.
>> Because in this case EMBOSS is wrapping primer3, that may not
>> be possible - but worth checking.
> Good idea to be careful - some (EMBASSY) wrappers pass the input file name
> directly but eprimer32 does read the sequence and then send it to primer3
> as a string.
> Any EMBOSS sequence input can be in the form asis::atcgatcgtagctgac which
> simply says the string is the sequence (rather than the file name). As the
> sequence has no name you can add:
> -sid myseqname
> to the command line which is then used in the output, and is also used to
> create the default output filename of myseqname.eprimer32
> The only limit will be the length of command line you are allowed on your
> system, so long sequences may fail. But that is a system (shell) limit -
> EMBOSS will read any length of sequence that is passed to it this way.
> regards,
> Peter Rice

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