[Biojava-dev] GFF3Reader modification

[Scooter Willis]

Carmelo

I can't ever to get SVN to cooperate either. I was able to pull the two additional files and Netbeans is now happy.

Scooter

From: Carmelo Foti <carmelo.foti86 at gmail.com<mailto:carmelo.foti86 at gmail.com>>
Date: Thursday, September 6, 2012 11:02 AM
To: Scooter Willis <hwillis at scripps.edu<mailto:hwillis at scripps.edu>>
Cc: Michael Heuer <heuermh at gmail.com<mailto:heuermh at gmail.com>>, "biojava-dev at lists.open-bio.org<mailto:biojava-dev at lists.open-bio.org>" <biojava-dev at lists.open-bio.org<mailto:biojava-dev at lists.open-bio.org>>
Subject: Re: [Biojava-dev] GFF3Reader modification

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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<tel:%28%2B39%29%20011%20090%207072>
>> Fax: (+39) 011 090 7099<tel:%28%2B39%29%20011%20090%207099>
>> E-mail: carmelo.foti at polito.it<mailto:carmelo.foti at polito.it>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org<mailto:biojava-dev at lists.open-bio.org>
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
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--
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<mailto:carmelo.foti at polito.it>