Annotate getSEQ weird behaviour.
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@giulio-di-giovanni-950
Last seen 9.6 years ago
Maybe it's only a temporary thing, but if I follow the help > library(annotate) Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > getSEQ("M22490") [1] "<html xmlns="\" <a="" href="&lt;a href=" http:="" www.w3.org="" 1999="" xhtml"="" rel="nofollow">http://www.w3.org/1999/xhtml" rel="nofollow">http://www.w3.org/1999/xhtml\""> <head xmlns:xi="\" <a="" href="&lt;a href=" http:="" www.w3.org="" 2001="" XInclude"="" rel="nofollow">http://www.w3.org/2001/XInclude" rel="nofollow">http://www.w3.org/2001/XInclude\""> <meta name="\" ncbi_app\""="" content="\" entrez\""=""/><meta name="\" ncbi_db\""="" content="\" nuccore\""=""/><meta name="\" ncbi_report\""="" content="\" fasta\""=""/><meta name="\" ncbi_format\""="" content="\" html\""=""/><meta name="\" ncbi_pagesize\""="" content="\" 20\""=""/><meta na...="" etc="" etc="" etc="" warning="" message:="" in="" readlines(paste("http:="" www.ncbi.nlm.nih.gov="" entrez="" batchseq.cgi?",="" :="" incomplete="" final="" line="" found="" on="" 'http:="" www.ncbi.nlm.nih.gov="" entrez="" b="" atchseq.cgi?cmd="&amp;txt=on&amp;save=&amp;cfm=&amp;list_uids=M22490&amp;db=nucleotide&amp;extr" afeat="16&amp;term=&amp;view=fasta&amp;dispmax=20&amp;SendTo=t&amp;__from=&amp;__to=&amp;__strand='"> > This it's weird, since only 3 days ago it was working perfectly. Any hints? NCBI changed the format of their entries and annotate package has still to be updated? Maybe it's me? my connection? Any suggestion will be appreciated, I really need it working with no errors now... Best, G [[alternative HTML version deleted]]
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@martin-morgan-1513
Last seen 6 weeks ago
United States
On 12/21/2010 08:40 PM, Giulio Di Giovanni wrote: > > Maybe it's only a temporary thing, but if I follow the help > > >> library(annotate) > Loading required package: AnnotationDbi > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > >> getSEQ("M22490") > [1] "<html xmlns="\" <a="" href="http://www.w3.org/1999/xhtml" rel="nofollow">http://www.w3.org/1999/xhtml\""> <head xmlns:xi="\" <a="" href="http://www.w3.org/2001/XInclude" rel="nofollow">http://www.w3.org/2001/XInclude\""> <meta name="\" ncbi_app\""="" content="\" entrez\""=""/><meta name="\" ncbi_db\""="" content="\" nuccore\""=""/><meta name="\" ncbi_report\""="" content="\" fasta\""=""/><meta name="\" ncbi_format\""="" content="\" html\""=""/><meta name="\" ncbi_pagesize\""="" content="\" 20\""=""/><meta na...="" etc="" etc="" etc=""> Warning message: > In readLines(paste("http://www.ncbi.nlm.nih.gov/entrez/batchseq.cgi?", : > incomplete final line found on 'http://www.ncbi.nlm.nih.gov/entrez /batchseq.cgi?cmd=&txt=on&save=&cfm=&list_uids=M22490&db=nucleotide&ex trafeat=16&term=&view=fasta&dispmax=20&SendTo=t&__from=&__to=&__strand =' >> >> > > > This it's weird, since only 3 days ago it was working perfectly. Hi Giulio -- no problems on my end; maybe your R or Bioconductor packages are out of date? More esoteric, but maybe encoding is an issue (?Sys.getlocale)? Martin > substr(getSEQ("M22490"), 1, 40) [1] "GGCAGAGGAGGAGGGAGGGAGGGAAGGAGCGCGGAGCCCG" > sessionInfo() R version 2.12.0 Patched (2010-11-21 r53647) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] annotate_1.28.0 AnnotationDbi_1.12.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] DBI_0.2-5 RSQLite_0.9-4 xtable_1.5-6 > > Any hints? NCBI changed the format of their entries and annotate package has still to be updated? Maybe it's me? my connection? > Any suggestion will be appreciated, I really need it working with no errors now... > > Best, > > G > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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