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

[Steve Lianoglou]

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