Along these lines, I took Kasper Hansen's df2GR() function and tarted it up
a bit, wrote a GR2df() function, and added some hooks to store the entire
works in a trivial (4-table plus views) database schema.  This stores
descriptions of what each track/range means, where it came from, and when
it was added, not unlike biomaRt.  (I had trouble finding "pickling"
functions for tracks and ranges so I rolled my own)  It's not perfect
(because I don't yet understand how to "bolt on" the appropriate BSgenome
so that out-of-memory sequence access is performed the way I want it to)
but it works well enough that I have started migrating other types of data
(segmented copynumber, gene-, splice-, exon-wise RNAseq, and BS-seq) into
freeze-dried GRanges.  If there is a better container schema in
GenomicFeatures::TranscriptDb, I'll switch to it today...

And since it's fresh in my mind, how does one automatically attach the
appropriate BSgenome to a GenomicRanges?  It seems like it should be
trivial, and the documentation hints at it, but I haven't succeeded yet in
doing this automatically.  I store the assembly from which a given GRanges
object's features were aligned, so if I can figure out the syntax, it's
done.

thanks all,

--t

On Thu, Feb 9, 2012 at 7:55 AM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> 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
>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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