[Bioperl-l] Nucleotide analysis modules - bugzilla # 1422

[Heikki Lehvaslaiho]

On Sun, 2003-06-22 at 06:03, Hilmar Lapp wrote:
> This stuff sounds very useful Rob. Would you be willing to commit this 
> yourself if we set you up with a CVS write account? Chris, if you read 
> this and you have a minute, could you set him up?
> 

Hilmar,

Rob is acting on my/public instructions on the namespace. We had the 
discussion some time ago.

I know that path is long but I think it is better to use named
namespaces than keep adding all kinds of stuff into Bio::Tools.  
I'd like to clean it properlyu at some point. 

Bioperl is getting so big - over 600 modules - that we really need to
keep distributing them in more explicitely named directories.
... in my opinion that is.
 
	-Heikki

> The long path is intimidating, but the naming makes sense. What do 
> others feel? I'm afraid Jason and Ewan are looking at other things 
> right now than their email ... If there is a single entry module for 
> the user, and <...>/RestrictionAnalysis.pm looks sounds like it could 
> be that, my suggestion would be to put that into Bio::Tools so that 
> people don't have too hard of a time finding it.
> 
> 	-hilmar
> 
> On Saturday, June 21, 2003, at 08:52  AM, Rob Edwards wrote:
> 
> > I have written a bunch of nucleotide analysis and manipulation modules 
> > that
> > I'd like someone to commit to the CVS for me.
> >
> > The modules are:
> >     * Bio/Seq/PrimedSeq.pm - a sequence object containing two primers
> >     * Bio/SeqFeature/Primer.pm - a representation of a single primer
> >     * Bio/Tools/Analysis/Nucleotide/Clone.pm - "clone" DNA and move 
> > sequence
> > features around
> >     * Bio/Tools/Analysis/Nucleotide/PCRSimulation.pm - simulate PCR
> >     * Bio/Tools/Analysis/Nucleotide/Primer3.pm - analyze primer3 output
> >     * Bio/Tools/Analysis/Nucleotide/Restriction/Enzyme.pm - a 
> > representation
> > of a single restriction enzyme
> >     * Bio/Tools/Analysis/Nucleotide/Restriction/EnzymeCollection.pm - a
> > representation of a bunch of enzymes
> >     * Bio/Tools/Analysis/Nucleotide/RestrictionAnalysis.pm - analyze
> > restriction sites in a DNA sequence
> >     * Bio/Tools/Run/Primer3.pm - run the Primer3 program.
> >
> > Some of these are based on a lot of work by others, and I have 
> > enhanced them.
> > In particular Bio/Tools/Analysis/Nucleotide/RestrictionAnalysis.pm 
> > should
> > replace Bio/Tools/RestrictionEnzyme.pm. The new module contains all 
> > that
> > functionality and has been extended to deal properly with redundant 
> > sequences
> > and with Bio/Tools/Analysis/Nucleotide/Restriction/EnzymeCollection.pm 
> > rebase
> > files can be parsed.
> >
> > I tried to write the pod to be compliant with the Pod Gods, and ran
> > maintenance/pod.pl -d Bio -v -b on these scripts - that should give me 
> > any
> > errors, right?
> >
> > In addition to the modules and test scripts there are a couple of 
> > examples
> > that will let you run primer3 to design primers, cut DNA with 
> > restriction
> > enzymes, and perform PCR and clone genes.
> >
> > Some of these modules address the bugs in bugzilla 1422:
> > http://bugzilla.bioperl.org/show_bug.cgi?id=1422
> >
> > The modules etc are available at
> > http://www.salmonella.org/bioperl/nucleotide_analyses.tgz
> >
> > If someone could commit them I'd be grateful.
> >
> > Thanks
> >
> > Rob
> >
> > _______________________________________________
> > 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
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