[EMBOSS] EMBOSS/Primer3

[Peter Rice]

On 15/10/2012 13:03, Ivaylo Stoimenov wrote:
> Hi,
>
> I am wondering if it is possible to pass some of the newest options to
> Primer 3, through EMBOSS eprimer32 wrapper. For example, an extremely
> useful option will be: "SEQUENCE_PRIMER_PAIR_OK_REGION_LIST=,,2950,50",
> which I am not sure how to address, especially in Python. Any suggestion
> how to turn this option on or any other additional argument for Primer3
> through eprimer32 interface?

Tricky. This option has a specific format, with start positions and 
lengths as the values. Values are in groups of 4, but there can be 
multiple groups. EMBOSS deliberately makes these kinds of options hard 
to define because they make web interfaces complicated.

Primer3 also has a web interface so we can check how they handle this 
option.... and they simply allow users to type in a string!

We can do a little better, as we can read in the values as ranges and 
convert to start and length values when we write the options for primer3.

For this option, which needs a pair of ranges, we can try adding two 
sets of ranges - one for the left and one for the right, and combine 
them when setting the option with any missing values defaulting to empty.

We may also be able to improve our handling of ranges for eprimer32. We 
require start,end to be specified because that is the EMBOSS style, but 
perhaps we can extend the syntax to allow start,+len or start+len for 
any range in EMBOSS. This seems to be an easy change to make.

I will try a few options and look to add something to the next release.

regards,

Peter Rice
EMBOSS Team