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 <rcava...@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]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
