Wow thanks for a serious testing file. There were some bugs and somewhat
interesting performance issues.

For example, I've discovered that gregexpr with fixed=TRUE is quadratic time
with respect to string length (gets real bad up in the millions). Haven't
been able to figure out why. This makes fixed=FALSE much quicker.
Counterintuitive. substring() is also surprisingly slow.

Anyway, try the latest SVN.  Or version 1.9.12.

Still much slower than read.delim. It's the attributes in the last column
(being translated to columns in R) that are so costly, and that one has them
in significant quantity. I guess I could give an option to disable that
parsing (or in general select the desired columns, as suggested previously),
but it should be much quicker for you now.

Thanks again,
Michael

On Fri, Oct 15, 2010 at 2:40 AM, Michael Dondrup <Michael.Dondrup@uni.no>wrote:

> Hi,
>
> I am trying to read in a genome annotation from a GFF3 file from NCBI [1]
> The file is about 7.5 MB and has ~17000 non-comment lines. While I can read
> the file
> with read.delim in less than a second, trying
> bsub = import.gff("~/Downloads/bsubtilis.gff")
> is very slow. I would rather like to use a standardized function form the
> package
> that understands various formats, but currently I cannot use it for whole
> genome
> annotation. Could this be improved, or is the fie format incorrect?
>
> Best
> Michael
>
>
> [1]:
> ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Bacillus_subtilis/AL009126.gff
>
> > sessionInfo()R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rtracklayer_1.8.1 RCurl_1.4-2       bitops_1.0-4.1
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0       Biostrings_2.16.0   BSgenome_1.16.1
> [4] GenomicRanges_1.0.9 IRanges_1.6.6       XML_3.1-0
> >
>
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