[BioC] Create transcriptDb using gff3 files? - library GenomicFeatures and rtracklayer

[Marc Carlson]

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.

  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.


   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 at gmail.com>  wrote:
>
>> Hi,
>>
>> On Tue, Apr 3, 2012 at 4:41 PM, Sang Chul Choi<schoi at 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
>>
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