[Bioc-devel] GenomeInfoDb::Seqinfo(genome) broken?

Vincent Carey stvjc at channing.harvard.edu
Thu Nov 3 13:19:06 CET 2016


On Thu, Nov 3, 2016 at 5:13 AM, Raymond Cavalcante <rcavalca at umich.edu>

> Hello,
> Sometime yesterday calls like GenomeInfoDb::Seqinfo(genome = 'hg19')
> stopped working with the error:
> > Error in file(file, "rt") : cannot open the connection
> From the documentation, that call relies on fetchExtendedChromInfoFromUCSC()
> and requires an internet connection, which I had and continue to have. I'm
> not really sure how to deal with this problem because the goldenPath link
> still works (http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/
> chromInfo.txt.gz <http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/
> chromInfo.txt.gz>), so something else is broken...
> Oddly, calls to rtracklayer::import.bed() that specify a genome work. I
> don't have any BSgenome packages installed where I'm running it, and from
> the documentation for genome, "An attempt will be made to derive the
> ‘seqinfo’ on the return value using either an installed BSgenome package or
> UCSC, if network access is available." So I would guess that
> rtracklayer::import.bed() would use the same fetchExtendedChromInfoFromUCSC
> ()...?
> On a related note, is there a non-BSgenome package that has the chromosome
> length / seqinfo information that doesn't require an internet connection
> (other than to download the package)? BSgenome is too large to require of
> users just for chromosome lengths. The org.db packages have chromosome
> lengths, but only with respect to one genome version for that organism, and
> from the documentation it isn't clear which version.
> Thanks,
> Raymond Cavalcante
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