[BioC] GenomicFeatures::makeTranscriptDbFromGTF?

[Steve Lianoglou]

Hey Michael,

I'll see if I can take a crack at it this w/e.

Also I'm in complete agreement w.r.t i/o stuff and your thoroughness
w/ rtracklayer is very much appreciated.

If we do have a centralized track i/o package that is outside of
rtracklayer, I nominate we name it bIO ... or something ;-)

... yes, I can hear the crickets ...

-steve

On Thu, Feb 9, 2012 at 4:48 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> 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 at 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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>
>



-- 
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