[Biojava-dev] GFF3Reader modification

[Carmelo Foti]

It seems that my eclipse doesn't love svn.
Sorry for the issue, i manually committed the new revision after a
successful "mvn test".
Let me know if there are any other issues, I'll fix asap.

Thanks,
Carmelo

2012/9/5 Scooter Willis <HWillis at scripps.edu>

> 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
> >_______________________________________________
> >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