[Bioperl-l] Using primer3

[Shawn Hoon]

On Wednesday, July 9, 2003, at 09:48  AM, Heikki Lehvaslaiho wrote:

>
> Shawn,
>
> It would be great if you could work on primer3 wrapper/parser.
>
> I am working on the Resriction modules and expect to do the first 
> commit
> any day now, so do not touch them.
>

  Before I start committing stuff, I'm not a heavy user of the Primer3 
parser and I haven't
seen any discussion on this AFAIK. Is it agreed that the new parser 
will replace the older
parser by Chad? It is backward compatible as far as I know since tests 
pass for the older t file.

if so I will need to replace Bio::Seq::PrimedSeq and 
Bio::SeqFeature::Primer as well.
In addition I will stick with the naming convention of 
Bio::Tools::Primer3 for the parser unless
there was some discussion that I missed on using 
Bio::Tools::Analysis::Nucleotide::Primer3 for that.



cheers,

shawn

> Thanks,
>
> 	-Heikki
>
>
>
> On Wed, 2003-07-09 at 09:32, Shawn Hoon wrote:
>> On Tuesday, July 8, 2003, at 02:26  AM, Mike Muratet wrote:
>>
>>> Greetings
>>>
>>> I'm trying to sort out running the primer3 methods in bioperl 1.2.1
>>> (the latest stable, isn't it?).
>>>
>>
>> bioperl 1.2.2 is just out available at:
>> http://www.bioperl.org/DIST/bioperl-1.2.2.tar.gz
>>
>> bioperl-run is available at:
>> http://www.bioperl.org/DIST/bioperl-run-1.2.2.tar.gz
>>
>>
>>> I see  by the README in Bio/Tools/Run that this is a separate branch,
>>> but I don't see at www.bioperl.org or CPAN where it can be 
>>> downloaded.
>>> (There is no Run::Primer3 that I can see in the directory.)
>>>
>>> I've looked through the wikis and searched the web, but I can't 
>>> figure
>>> out how to use it. I know it's a simple answer, could someone clue me
>>> in?
>>>
>>
>> Currently Primer3 has no wrapper in bioperl-run. However I managed to
>> dig up an April Email by Rob
>> that has a link to some modules that he has written for working with
>> Primer3.
>>
>> http://www.salmonella.org/bioperl/primer3_v0.3.tgz
>>
>> Rob I can integrate this with bioperl-run if its okay with you.
>> Are you still having problems with the WrapperBase I/O handling?
>>
>> cheers,
>>
>> shawn
>> .
>>
>>> Thanks
>>>
>>> Mike_______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> ___ _/_/_/_/_/________________________________________________________
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>