[BioPython] Emboss eprimer3

[Stefanie Lück]

Hi!

I got a patch to add a '-originalformat' argument. If someone is interested 
too, I could send it to him or the mailing list.

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

This is no problem. I just need the data ;-)

>>> I don't know if there is a primer3 argument for limiting the G or C's at 
>>> the end - have you asked on the EMBOSS mailing list?

Yes, no answer yet.

Kind regards
Stefanie



----- Original Message ----- 
From: "Peter" <biopython at maubp.freeserve.co.uk>
To: "Stefanie Lück" <lueck at ipk-gatersleben.de>
Cc: <biopython at lists.open-bio.org>
Sent: Tuesday, March 24, 2009 11:00 AM
Subject: Re: [BioPython] Emboss eprimer3


2009/3/24 Stefanie Lück <lueck at ipk-gatersleben.de>:
> Hi!
>
> I have some questions about eprimer3 from Emboss which I use over Python 
> to design primers in a batch mode:
>
> 1) I'm using the GCclamp function (value=1). Is it possible to limit the G 
> or C's at the end to maximum of one G or C?

OK, you're using the gcclamp argument (i.e. GC clamp), which is
supported by the Bio.Emboss.Applications wrapper.
http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/eprimer3.html

I don't know if there is a primer3 argument for limiting the G or C's
at the end - have you asked on the EMBOSS mailing list?

> 2) Is there a setting to get the original primer3 output? The emboss 
> output is for hundrets of primers not very usefull and many informations 
> are missing.

>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.

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

Peter