[BioC] GenomicFeatures::makeTranscriptDbFromGTF?

[Steve Lianoglou]

Hi,

I thought it would be handy to make a GenomicFeatures::TranscriptDb
from a gtf file and was somehow surprised to see that I couldn't find
such a function in GenomicFeatures.

I'm happy to whip up such a function, but wanted to check in to make
sure I'm not missing something like (1) you can already do it; or (2)
it's not as straightforward as I think; (3) maybe it's there and I'm
not looking hard enough.

Right now I just want to build it on the gff that the knew versions of
tophat build when you pass in a gtf/gff file of known transcripts (the
--G/--GTF cmd line arg), but I think it'd be handy overall.

I don't think gff/gtf's have any column for exon ordering, though, in
which case I'd just assume the exons are ordered linearly (bye bye
trans-splicing)).

Good idea? Bad idea? Already done?

-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