[Biojava-dev] DNASequence and reverse complement

[Andreas Prlic]

Hi Michael and Hannes,

just to add... any contributions to add more features to the DNA side of
BioJava 3 would be great!

Michael, what features of legacy are you using, that have not been ported
to v3?

Andreas


On Wed, May 1, 2013 at 9:53 AM, Michael Heuer <heuermh at gmail.com> wrote:

> Hello Hannes,
>
> I am afraid you may be right; that is why I still use biojava-legacy
> most of the time.
>
> I reached out to the author of these recently
>
> https://github.com/timpalpant/java-genomics-io
> https://github.com/timpalpant/java-genomics-toolkit
>
> to see if he may be interested in contributing to biojava but have not
> received a response.  There may also be some utility code in Picard,
> the open source fork of GATK, and possibly GenomeSpace that would be a
> better fit in biojava, if anyone knows contributors to those projects.
>
> A java client to the new Ensembl REST APIs would also be useful
>
> http://beta.rest.ensembl.org/
>
>    michael
>
>
> On Wed, May 1, 2013 at 11:41 AM, Hannes Brandstätter-Müller
> <biojava at hannes.oib.com> wrote:
> > Yeah, I get the feeling that the support for proteins is way more fleshed
> > out than the support for sequencing…
> >
> > I will try to experiment around with the code and see if I need to "fix"
> > something in the core too for my use-case.
> >
> >
> >
> >
> > On Wed, May 1, 2013 at 5:14 PM, Scooter Willis <HWillis at scripps.edu>
> wrote:
> >
> >>  The features is designed to be flexible as a place holder based on
> >> position for other data. So you can optimize based on the data you need
> to
> >> store.
> >>
> >> Not sure any testing was done on maintaing features when returning
> >> different views of the sequence without looking at the code. An original
> >> goal was to maintain that linkage going from chromosome dna rna amino
> acid
> >> as an example.
> >>
> >>
> >>
> >>
> >>
> >> -------- Original message --------
> >> From: Hannes Brandstätter-Müller <biojava at hannes.oib.com>
> >> Date: 05/01/2013 10:43 AM (GMT-05:00)
> >> To: biojava-dev <biojava-dev at lists.open-bio.org>
> >> Subject: [Biojava-dev] DNASequence and reverse complement
> >>
> >>
> >> Hi,
> >>
> >> I am a bit unclear about DNASequence and Features in biojava3...
> >> Say I want to attach meta info to a sequence (like quality scores for
> >> fastq, or other numbers to single bases, how would be the intended or
> best
> >> way be?
> >> Single features for each base? One Feature holding a list of values?
> >>
> >> Following that, what if I need a reverse complement DNASequence from the
> >> previous sequence, how would I do that? The reverseComplement() "only"
> >> gives me a SequenceView, and how would I ensure the attached values from
> >> the Feature stay consistent?
> >>
> >> Hannes
> >> _______________________________________________
> >> biojava-dev mailing list
> >> biojava-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >>
> >
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