Is there anything makeTranscriptDbFromGFF could do to help with this?
Sounds like you typically want something like a TxDb, except perhaps with
some special considerations. Following the NCBI conventions is probably
worth it.


On Wed, Jul 16, 2014 at 8:58 AM, Chris Stubben <stubben@lanl.gov> wrote:

> I would also suggest using rtracklayer import or create a genome data
> package.   At least for microbial genomes, you often just need to return
> features (CDS, pseudogenes, tRNAs, etc) that have a parent with a locus_tag
> key and assign that locus tag to the child (the read.gff default), so
> that's what is getting messed up with your large file.
> I'll probably use the rtracklayer import object in future versions instead
> and then join on Parent where locus_tag is NA to the ID where locus_tag is
> not NA.
> Chris
>
>
>
>  I cc'd the packageMaintainer(), so that they are more likely to see this
>> post.
>>
>
>  I don't know whether this helps in this particular case, but packages
>> should be using rtracklayer::import rather than creating their own readers.
>> Then at least whatever deficiencies are identified and corrected benefit
>> the entire project.
>>
>
>
>
>
> --
>
> Chris Stubben
>
> Los Alamos National Lab
> Bioscience Division
> MS M888
> Los Alamos, NM 87545
>
> Phone: (505) 667-3295
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.
> science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

