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

[Scooter Willis]

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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