[Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer

[Elia Stupka]

Hi Robert,

Good to see Primer3 coming along, some comments:

you might want to have a look at bioperl-run. We have decided to split 
the actual "running" of programs from their parsing, so in theory you 
should have a Bio::Tools::Run::Primer3 that inherits from 
Bio::Tools::Run::WrapperBase and has some standard methods such as run 
(I notice you call the method exc, but the doc title is run...). Also 
all the arguments can then be simply put in a begin block as arrays of 
keyowrds which get "authorized" to be used by the OK_FIELD hash (see 
any of the run modules in bioperl-run for more specs).

Then the parser would go into Bio::Tools::Primer3 only for the parsing 
methods, which would be at least the basic next_result method shared by 
other Tool parsing modules (though admittedly we haven't yet come up 
with a proper interface module or base class)

Elia



On Friday, Mar 21, 2003, at 14:12 Asia/Singapore, Rob Edwards wrote:

> Hi all,
>
> I needed to design some primers with primer3, and as the current 
> modules were
> outlines I took Chad Matsalla's work and built on it.
>
> I have enhanced the three modules that were started:
> Bio::Seq::PrimedSeq is a representation of a sequence with two primers
> attached.
> Bio::SeqFeature::Primer is a single primer that can be associated with 
> a
> sequence using PrimedSeq
> Bio::Tools::Primer3 is a wrapper for the primer3 program
> (http://www-genome.wi.mit.edu/genome_software/other/primer3.html)
>
> I spent most effort working on Primer3.pm which now will run primer3, 
> as well
> as pass all the arguments you'd like (and perhaps some you 
> wouldn't.....?) It
> will also return the results as raw feed, one primer at a time, or a 
> stream
> of PrimedSeq objects that can be parsed out. The two example scripts
> demonstrate these at work.
>
> There are some areas that are not truly bioperly yet, but I am working 
> on it
> and gettting my way around it. At least the docs are complete.
>
> Please take a look at these and see if they are worthy of including at 
> some
> point in the future. All pointers as to what I should improve are 
> appreciated.
>
> The modules and scripts are available from
> http://www.salmonella.org/bioperl/primer_0.1.tgz Give them a try and 
> see what
> you think!
>
>
> Rob
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> Bioperl-l at bioperl.org
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>
>
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