[BioPython] Emboss eprimer3
Chris Fields
cjfields at illinois.edu
Tue Mar 24 16:51:32 UTC 2009
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
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