[BioPython] Emboss eprimer3

[Chris Fields]

On Mar 24, 2009, at 5:00 AM, Peter wrote:

> ...
>> From reading the documentation there is a "fformat1" argument which
> *might* do what you want - you could try this out on the command line
> and see.  Note that this argument is not currently supported in the
> Bio.Emboss.Applications wrapper, but that would be easy to add.  If
> this argument doesn't do what you want, you'd have to ask the EMBOSS
> people about alternative output formats. Alternatively, you might
> investigate the original Whitehead version of primer3.

Peter,

Not sure if this will be a problem for the BioPython wrapper for  
primer3, but the latest Primer3 version on Sourceforge (v2.0.0a)  
radically changes the various input parameters.  I had to rewrite a  
bunch of code to handle those as well as older (v1) primer3 params.

> Note that if you do succeed in changing the output format, you may
> need a new parser to read it.
>
> Peter

primer3 input and output is BoulderIO (which I think is an essentially  
obsolete format Lincoln Stein wrote up many years ago).  It's very  
easy to parse, just simple key-value pairings.

chris