Hi, just installes R 2.12.0 biocondutor 2.7 rtracklayer 1.10 and I can confirm that there is a major improvement in the speed of import.gff. Thanks a lot for this fix. Michael On Oct 16, 2010, at 6:39 AM, Michael Lawrence wrote: > 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 at="" 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_subtil is/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 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > Michael Dondrup Post-doctoral researcher Uni BCCS Thorm?hlensgate 55, N-5008 Bergen, Norway Phone: +47 55584157 Fax: +47 55584354 Please note my new phone number