[Bioperl-l] simplealign, prediction parselist
Heikki Lehvaslaiho
heikki@ebi.ac.uk
18 Sep 2002 09:29:32 +0100
Rickhard,
The recommended way to contribute is to first post descriptions of
modules, names and methods, for other people to comment on. Then in
addition to writing the actual code, you are expected to write test
suite (into t directory) with necessary data files (into t/data) which
test at least all public methods in the modules. The actual commit can
be handled by any of the core developer or anyone with a CVS account. If
your contributions to bioperl are more than one off, we'd eventually
like to give you a CVS account, so that you can maintain and add to the
code base yourself.
To start with, it is best that you post everything to the list.
-Heikki
On Tue, 2002-09-17 at 20:57, Richard Adams wrote:
> Heikki,
> I'll tidy up the Simple::Align->purge code and send it to you asap.
> Re parsers for netphos, psort etc. Basically I'm working with about 30-40
> genes on chromosome 4
> in a region associated with bipolar disorder. I'm trying to build up a
> database of possibly important
> functional residues/regions of the proteins for prioritising the
> experimental analysis of SNPs within
> the coding region of the genes. Also I'm hoping to bolster the prediction
> accuracy of these
> programs by looking for conservation of prediction between sequence
> homologues in a Clustal alignment.
>
> So that's why I'm developing the parsers. At present they are not in the
> BioPerl 'format' at all and are standalone
> modules/subroutines. I've not contributed to BioPerl before - is there a
> standard way that you want code contributed in
> or is some assistance likely to be available from someone more experienced
> with BioPerl guts than myself?
>
> Richard
>
> Heikki Lehvaslaiho wrote:
>
> > Richard,
> >
> > Bio::SimpleAlign::purge() has not been functional as far as I know. We
> > do not even have tests for it. Please send me your fixes and add them in
> > and add you as an contributor to the module.
> > It would be even better of you have written tests into t/SimpleAlign.t,
> > too!
> >
> > It has been a while since you posted your message and there has been no
> > answers to it. I think it can be safely said that no one else is working
> > on Psort, TargetP or netphos parsers. It would be great to have them.
> > Let us know what your plans are.
> >
> > -Heikki
> >
> > On Tue, 2002-08-27 at 11:51, Richard Adams wrote:
> > > Hello,
> > > Please ignore this if it's already been fixed but there seems to be 2
> > > problems in 1.0.2
> > > with Bio::SimpleAlign purge function.
> > >
> > > 1. the get_nse call produces the error
> > > Use of uninitialized value in numeric eq (==) at
> > > /packages/perl/lib/site_perl/5.6.0/Bio/SimpleAlign.pm line 373, <GEN0>
> > > line 242.
> > > 2.
> > > the lines
> > > @one = $seq->seq();
> > > @two = $seq2->seq();
> > > I guess are supposed to be split so that each element is an amino
> > > acid or - or .
> > > But the way the code works there will only be one element - the
> > > whole sequence string.
> > >
> > > I've fixed these problems for my own use so if my code would be any use
> > > I'd gladly submit it.
> > >
> > >
> > >
> > > I'm writing some parsers for various prediction servers, such as
> > > Expasy's Psort, TargetP, netphos and ultimately plan to develop parsers
> > > for some secondary
> > > structure prediction servers. Are people already working on this sort
> > > of thing or would these be useful additions?
> > >
> > > Richard
> > >
> > > Dr Richard Adams
> > > Molecular Medicine Centre
> > > University of Edinburgh UK
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > --
> > ______ _/ _/_____________________________________________________
> > _/ _/ http://www.ebi.ac.uk/mutations/
> > _/ _/ _/ Heikki Lehvaslaiho heikki@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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--
______ _/ _/_____________________________________________________
_/ _/ http://www.ebi.ac.uk/mutations/
_/ _/ _/ Heikki Lehvaslaiho heikki@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
___ _/_/_/_/_/________________________________________________________