[Biojava-dev] I would like to take ownership of Port genbank parser from biojava 1 to biojava 3

[Spencer Bliven]

The genome module does seem like a reasonable place for the genbank parser.
I think it's rather too late to move the FastaParser out of core, since
it's so widely used. We should be wary of having module bloat going
forward, although I do support keeping core lean and to the point.


On Thu, Jun 20, 2013 at 9:48 AM, Scooter Willis <HWillis at scripps.edu> wrote:

> Probably better to minimize changes and access to core to keep it stable
> and small. Similar parsing of data types for gff and gtf as annotated data
> so could go in org.biojava3.genome.parsers.genbank. By the same argument
> the FASTA reader/writer should be moved out of core and moved into a
> package that deals with sequence-unannotated data.
>
> Scooter
>
>
>
>
> On 6/20/13 11:25 AM, "Michael Heuer" <heuermh at gmail.com> wrote:
>
> >Hello Charles,
> >
> >Sounds good, but the target package you want is
> >
> >org.biojava3.core.sequence.io
> >
> >   michael
> >
> >
> >On Thu, Jun 20, 2013 at 12:22 AM, Charles Stockman
> ><chuck.stockman at yahoo.com> wrote:
> >> Before I ask my question(s) let me thank Andreas Prloic for his help in
> >>getting my started.
> >>
> >> I believe that I am ready to start my first bug.  The bug that chosen is
> >>
> >> Port genbank parser from biojava 1 to biojava 3, but I have a few
> >>questions.
> >>
> >> 1. How can I get this enhancement assigned to me.
> >>
> >> 2. After looking over the code the legacy code, I believe the best goal
> >>is to
> >>
> >>
> >>     port the test files starting with Genbank from directory
> >>
> >>
> >>biojava-legacy-1.8.2-src/core/src/test/java/org/biojavax/bio/seq/io
> >>
> >>     To the new directory in biojava 3
> >>
> >>
> >>             org.biojava3.sequencing.io.genbank and
> >>org.biojava3.sequencing..io.genbank.
> >>
> >> I will port both the source cost and the files that will be tested.
> >>
> >> 3. While I am porting the code, is there any other bugs/enhancement
> >>that I should also work into the port.
> >>
> >> Thank you very much for your help
> >>
> >> Charles Stockman
> >> _______________________________________________
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> >> biojava-dev at lists.open-bio.org
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