[Biojava-dev] GFF3Reader modification

[Scooter Willis]

Carmelo

Looks like you did a code check in for biojava3-genome updating
FeatureList. You have a getAttributes() that is not a method of FeatureI.
Can you make sure all the changed code is checked in and everything
compiles? I have a need to build a list of ordered genes based on
chromosomal location so was going to try building the list using a
gff/gff3 annotation file for the human genome. Will see if I can help on
any performance issues.

Thanks

Scooter

On 8/22/12 4:00 PM, "Michael Heuer" <heuermh at gmail.com> wrote:

>Hello Ryan, Carmelo
>
>I have somewhere on the back burner a wish to support GFF3+GVF and add
>low-level streaming APIs to GFF3 parsing as was done for FASTQ
>parsing.  Let me know if this sounds useful and I will try to get on
>it sooner.
>
>   michael
>
>
>On Wed, Aug 22, 2012 at 2:48 PM, Carmelo Foti <carmelo.foti86 at gmail.com>
>wrote:
>> Hi Ryan,
>>
>> I made some changes in the GFF3Reader class, but I had internet issues
>>and
>> I could not commit the patch.
>> I think it would be better for you to start from the updated version,
>>which
>> is a lot faster when using the entire hg19 gtf.
>> I'll send you the files as soon as possible
>>
>> Regards,
>> Carmelo Foti
>>
>> 2012/8/22 Ryan Golhar <ngsbioinformatics at gmail.com>
>>
>>> Hi all - I'm using the GFF3Reader right now to read in the hg19 GTF
>>>file
>>> from UCSC.  In debugging my own application, loading the GTF file take
>>>a
>>> little bit of time. I'd like to make a modification to read each line
>>>on
>>> demand instead of all at once.  Is this something others would find
>>>useful?
>>>  If so, I'll submit a patch with my change.
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>
>>
>>
>>
>> --
>> Carmelo Foti
>> Research assistant
>> Politecnico di Torino
>> Dipartimento di Automatica e Informatica - EDA Group
>> C.so Duca degli Abruzzi 24, 10129 Torino (ITALY)
>> Phone: (+39) 011 090 7072
>> Fax: (+39) 011 090 7099
>> E-mail: carmelo.foti at polito.it
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
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