[BioPython] Emboss eprimer3

[Brad Chapman]

Hi all;

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

Is this a patch to EMBOSS itself? If so, did the developers indicate
it would be in future versions of EMBOSS?

If that's the case, we can easily add this option to the commandline
interface. You need a:

           _Option(["-originalformat"], ["input"], None, 0),

line in Bio.Emboss.Applications.Primer3Commandline.

> >>>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 ;-)

Out of curiosity, what parameter did you find useful from that
output that is not in the eprimer3 format output?

> >>> 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.

What I do in cases like this is ask for more primers
(-numreturn) and then post-parse them to pull out the ones that
satisfy my additional criteria. The output is ordered by primer3's
ranking, so the first one that passes the criteria would move on.
If none are satisfactory, then you can also build in a logic to
decide if any are good enough for your use (for example, 2 G/Cs at
the end) and pick one from this remaining group with less stringency.

Brad



> 
> 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
> 
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