[Bioc-devel] GenomeInfoDb::Seqinfo(genome) broken?
rcavalca at umich.edu
Thu Nov 3 20:58:46 CET 2016
Awesome, thanks for the quick fix!
> On Nov 3, 2016, at 14:50, Hervé Pagès <hpages at fredhutch.org> wrote:
> 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.
>> 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
>>> On Thu, Nov 3, 2016 at 5:13 AM, Raymond Cavalcante
>>> <rcavalca at umich.edu> wrote:
>>>> 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
>>>> 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
>>>> 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.
>>>> Raymond Cavalcante
>>>> [[alternative HTML version deleted]]
>>>> Bioc-devel at r-project.org mailing list
>>> Bioc-devel at r-project.org mailing list
> Hervé Pagès
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> E-mail: hpages at fredhutch.org
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