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

[Hilmar Lapp]

> -----Original Message-----
> From: Heikki Lehvaslaiho [mailto:heikki at ebi.ac.uk] 
> Sent: Monday, June 23, 2003 1:50 AM
> > 
> 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. 
> 

I do agree in general, but I am concerned that people have a harder time
then getting an overview on what is there.

Right now, if you're looking for something that parses output of some
sort or emulates some tool, you look into Bio::Tools and if there's
nothing there named in a way that rings a bell with you then it doesn't
exist.

If that doesn't work anymore, there will have to be a table of supported
tools and what the entry module is, and that table will have to be kept
up to date and easily accessible, which essentially means it there needs
to be something like Bio/Tools.pm that merely contains POD documenting
what to find where.

What concerns me is keeping this Bio/Tools.pm up to date. What would be
cool if there was a script that regularly scans all modules under the
Bio::Tools hierarchy and constructs the aforementioned table, possibly
by recognizing some special tags that tell it that this module is an
entry module and what its purpose is.

What are your thoughts on this?

	-hilmar

> 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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