[Biojava-dev] DNASequence and reverse complement

[Michael Heuer]

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
>>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev