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

Hervé Pagès hpages at fredhutch.org
Thu Nov 3 19:50:28 CET 2016

Should now be fixed in release (GenomeInfoDb 1.10.1) and devel
(GenomeInfoDb 1.11.2).


On 11/03/2016 11:12 AM, Hervé Pagès wrote:
> I'll look at this. I think Seqinfo(genome="hg19") needs to query
> NCBI to get some information (e.g. SequenceRole) that allows ordering
> the sequences in the returned Seqinfo in the "natural" order.
> H.
> On 11/03/2016 05:47 AM, Michael Lawrence wrote:
>> I think this is because the NCBI server switched to https (via a
>> redirect that I guess the R url() connection fails to follow). The
>> reason rtracklayer still works is that it's only querying UCSC.
>> GenomeInfoDb also queries NCBI to get the mappings to the NCBI
>> seqlevels. Does that really need to happen when only getting the
>> Seqinfo?
>> On Thu, Nov 3, 2016 at 5:13 AM, Raymond Cavalcante
>> <rcavalca at umich.edu> wrote:
>>> 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
>>>         [[alternative HTML version deleted]]
>>> _______________________________________________
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
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