Hi Steve,

I had thought someone would want something like this, and it would be nice
to able to parse a GTF file into something more useful than a GRanges, as
rtracklayer supports now.

So I'd definitely encourage you to go ahead, while recommending that it be
based on the import.gtf function in rtracklayer.

We really need to have a centralized track I/O package. I'm not sure why,
but everyone seems intent on writing the same parser over and over again.
Duplicated effort frustrates me. It doesn't have to be rtracklayer, but
somewhere in the infrastructure we need reliable I/O that handles all of
the corner cases. I've embarked on a time consuming effort of implementing
a comprehensive test suite for rtracklayer, which should make it at least a
base for such a package.

Thanks a lot for volunteering this contribution,
Michael

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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