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

[Raymond Cavalcante]

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).
> 
> H.
> 
> 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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>>> 
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>> 
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
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