On Wed, Apr 4, 2012 at 5:44 PM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> I was looking at this during the course, and this is on my TODO list for
> the next release cycle.  I think it is long overdue and I don't think that
> the community is going to get it done in spite of all the enthusiasm.
>  There has not been time to do it before now but I am hoping that will now
> change.  It should be simple enough in principle, but it might not be
> exactly trivial as I have discovered (on closer inspection) that the gff
> specification is not as concrete as one would like it to be.  Also there
> have been several different versions.
>
> Some things that can help speed me along:
>
> 1) which version is most important?  gff3?  Or one of the other versions?
>  It is likely that with the older versions we may not be able to extract as
> much meaningful information.
>
>

There are really only two ways to encode a real gene model in GFF. One is
using GFF3 (with the conventions defined in the spec), and the other is to
use GTF, which is layered on top of GFF2 (Sanger's version of the format).
GFF3 is cleaner than GTF in my opinion.


>  2) where is the best place to find some typical gff3 files for examples?
>  This should not be difficult, but when I was looking before I was finding
> that people were surprisingly stingy about sharing these.
>
>
I would recommend simply dumping out some of the TranscriptDb objects using
rtracklayer. I have had no trouble feeding those files to other tools and
having them be parsed, processed and displayed correctly.

If you have any questions about the spec, just ask. I've read it over many
times.


>
>  Marc
>
>
>
>
> On 04/03/2012 03:57 PM, Michael Lawrence wrote:
>
>> Marc was working on this during the course in Feb. Not sure what happened
>> to it. He said it was simple. Maybe just waiting for the release to pass.
>>
>> Michael
>>
>> On Tue, Apr 3, 2012 at 3:40 PM, Steve Lianoglou<
>> mailinglist.honeypot@gmail.com**>  wrote:
>>
>>  Hi,
>>>
>>> On Tue, Apr 3, 2012 at 4:41 PM, Sang Chul Choi<schoi@cornell.edu>
>>>  wrote:
>>>
>>>> Hi,
>>>>
>>>> I am wondering if I could create a TranscriptDb object (library
>>>>
>>> GenomicFeatures) using a gff3 file.  I could read a gff3 file using
>>> import.gff3, but I could not find a way to create TranscriptDb object
>>> from
>>> the object from import.gff3.
>>>
>>>> Two arguments for makeTranscriptDb are required: transcripts, splicings.
>>>>
>>> It does not seem to be easy to parse this information from the object
>>> form
>>> import.gff3.  I will appreciate any help.
>>>
>>> As far as I know, this functionality isn't there yet ...
>>>
>>> I once (early feb, 2012) suggested I might take a crack at making this
>>> happen but haven't actually found the time to do it ... I'm not sure
>>> anyone in bioc-core land (hi, Marc) has found the time to do it
>>> either, so I think you're out of luck.
>>>
>>> Sorry for that. But the good news is that I bet a patch that does this
>>> would be welcome ;-)
>>>
>>> -steve
>>>
>>> --
>>> Steve Lianoglou
>>> Graduate Student: Computational Systems Biology
>>>  | Memorial Sloan-Kettering Cancer Center
>>>  | Weill Medical College of Cornell University
>>> Contact Info: http://cbio.mskcc.org/~lianos/**contact<http://cbio.mskcc.org/%7Elianos/contact>
>>>
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