[BioC] NCBI gff3 annotation file and read.gff()

[Martin Morgan]

On 07/16/2014 05:05 AM, Ugo Borello wrote:
> Hi,
>
> I am trying to read without success, a gff file downloaded from the NCBI
> genomes ftp directory.
>
> library("genomes")
>> annot <-
> read.gff('~/Desktop/NCBI_Anno/ref_Macaca_fascicularis_5.0_top_level.gff3')
> Error in `$<-.data.frame`(`*tmp*`, "description", value = "") :
>    replacement has 1 row, data has 0

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.

Martin

>
> Any hint/help?
>
> Thank you
>
> Ugo
>
>
>
>
>> sessionInfo()
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
>   [1] genomes_2.10.0       Biostrings_2.32.1    XVector_0.4.0
> GenomicRanges_1.16.3 GenomeInfoDb_1.0.2
>   [6] IRanges_1.22.9       BiocGenerics_0.10.0  RCurl_1.95-4.1
> bitops_1.0-6         XML_3.98-1.1
>
> loaded via a namespace (and not attached):
> [1] stats4_3.1.1    tools_3.1.1     zlibbioc_1.10.0
>
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