Hi Michael, This has been fixed now in the dev version of biomaRt. Available here: http://bioconductor.org/packages/2.8/bioc/html/biomaRt.html Cheers, Steffen On Fri, Apr 1, 2011 at 1:24 AM, mmaguire <mmaguire at="" ebi.ac.uk=""> wrote: > Thanks, Steffen, I've forwarded the mail to Rhoda, our Biomart person. > Apologies for the typo re "mart", copy-and-paste followed mis-type! > > Cheers > > Mick >> Michael Maguire >> Variation Archive Bioinformatician >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD >> >> Phone +44 1223 494674 >> Email mmaguire at ebi.ac.uk > > On Apr 1, 2011, at 12:41 AM, Steffen Durinck wrote: > >> Thanks Mike, Wolfgang, >> >> It looks like this should be an easy fix in biomaRt. We're currently >> reading in the text connection as follows in biomaRt: >> >> read.table(con, sep = "\t", header = FALSE, quote = "", comment.char = >> "", stringsAsFactors = FALSE) >> >> if we change this to: >> >> read.table(con, sep = "\t", header = FALSE, quote = "\"", comment.char >> = "", stringsAsFactors = FALSE) >> >> I think it should work. ?I'll fix biomaRt and provide a new dev >> version within the next few days. >> >> Cheers, >> Steffen >> >> On Thu, Mar 31, 2011 at 3:52 PM, Wolfgang Huber <whuber at="" embl.de=""> wrote: >>> Dear Mick >>> >>> thank you for the (almost - see below) reproducible report. >>> >>> The bottomline is that R's read.table does not like newline (\n) characters >>> within quoted text ("), interpretes them as line ends, which messes up the >>> tab-delimited table that the BioMart query returns. >>> >>> I suggest either of two possible solutions: >>> - The BioMart dataset is modified to abstain from putting \n and other funny >>> characters within quoted text >>> - the biomaRt package is modified to tolerate such behaviour >>> >>> I am not sure how it would be possible to make the communication between >>> BioMart servers and its clients such as biomaRt more robust. Is there a >>> clear specification of BioMart servers' tab-delimited format and what the >>> legal characters are? This would certainly be helpful for people who program >>> clients. >>> >>> I compacted your example into the following. >>> >>> >>> ?library("biomaRt") >>> ?options(error=recover) >>> >>> ?ensembl.var <- useMart("snp") >>> ?sv <- useDataset("hsapiens_structvar", mart=ensembl.var) >>> >>> ?x2 <- getBM(c("chrom_start", "chrom_end", >>> ? ? ? ? ? "structural_variation_name", "description"), >>> ? ? ? ? ? ?filters=c("chr_name"), values=list(6), mart=sv) >>> >>> >>> This generates the "error in scan(file, what, nmax, sep, dec, quote, skip, >>> nlines, na.strings, : line 135 did not have 4 elements". You then get a menu >>> from R's debugger. Enter "4" to get into the local evaluation environment of >>> the getBM function just before the error is thrown. Then, type >>> >>> ?cat(postRes, file="postRes.txt") >>> >>> and open the file in a text editor, e.g. emacs. Lines 133-135 is: >>> 269735 ?349386 ?esv29987 ? ? ? ?Levy 2007 "The diploid genome sequence of an >>> individual human. >>> >>> " PMID:17803354 [remapped from build NCBI36] >>> >>> Note that there are two newlines (\n) within the title of the paper, which >>> probably shouldn't be there. The same is also true at many other places in >>> the file, whenever the Levy paper is refered. >>> >>> I leave it to Steffen to decide whether he wants to modify biomaRt; and to >>> you, whether you want to lobby with the curators of that dataset to put more >>> consistency in the 'description' field. >>> >>> Hope this helps. >>> >>> ? ? ? ?Wolfgang >>> >>> PS: The line from your example code >>> ? useMart("snps") >>> resulted for me in an error message "Incorrect BioMart name, use the >>> listMarts function to see which BioMart databases are available". (There is >>> an extraneous "s"). Next time, please always send an exact transcript of >>> what you do, to make sure the problem is not due to a typing error. >>> >>> >>> >>> Second, and more to the point of your question, t >>> Il Mar/31/11 5:25 PM, mmaguire ha scritto: >>>> >>>> To whom it may concern, >>>> I work in the DGVa group at EBI, this group works on structural variants. >>>> ?I ran into a problem using the R package biomaRt when attempting to >>>> retrieve information from the "snps" mart "hsapiens_structvar" dataset, >>>> here is my code with comments: >>>> >>>> Here is the R code that I've written: >>>> >>>> # Testing retrieval of SVs from Biomart >>>> >>>> library(biomaRt) >>>> >>>> # Select the version "ENSEMBL ?VARIATION 61 (SANGER UK)" >>>> ensembl.var<- useMart("snps") >>>> >>>> # Select SV dataset from the chosen mart >>>> sv<- useDataset("hsapiens_structvar", mart=ensembl.var) >>>> >>>> # Set attributes and filters for the chosen dataset and retrieve the data >>>> into a data frame >>>> chr6.svs<-getBM(c("chrom_start", "chrom_end", >>>> "structural_variation_name"), filters=c("chr_name"), values=list(6), >>>> mart=sv) >>>> # Check for returned data (brings back 65,532 rows for chromosome 6) >>>> summary(chr6.svs) >>>> # Write the data frame to a text file >>>> write.table( ?chr6.svs, file='chr6_svs_from_biomart.txt', sep="\t", >>>> quote=FALSE, append=FALSE, na="", row.names=FALSE ) >>>> >>>> >>>> # Adding "description" to the vector of attributes in the above call to >>>> function "getBM()" causes the code to fail with the error given below. >>>> chr6.svs<- getBM(c("chrom_start", "chrom_end", >>>> "structural_variation_name", "description"), filters=c("chr_name"), >>>> values=list(6), mart=sv) # Does not work >>>> #Error returned by R when attempting to get the SV description attribute: >>>> # Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, >>>> na.strings, ?: >>>> # ?line 135 did not have 4 elements >>>> >>>> The code fails when the SV "description" attribute is added. ?I think the >>>> problem arises due to the spaces in the "description" field with R >>>> incorrectly interpreting each space delimited word as vector element. ?My R >>>> is limited so I may be wrong. ?Anyway, I can run the same query from the web >>>> interface and correctly retrieve the "description" attribute. >>>> I've checked this with our Biomart person, Rhoda Kinsella, and the data in >>>> the Biomart looks correct and, as stated above, we can export it from the >>>> web interface. >>>> Any help gratefully received. >>>> >>>> Cheers >>>> >>>> Mick >>>> >>>>> Michael Maguire >>>>> Variation Archive Bioinformatician >>>>> European Bioinformatics Institute >>>>> Wellcome Trust Genome Campus >>>>> Hinxton >>>>> Cambridge CB10 1SD >>>>> >>>>> Phone +44 1223 494674 >>>>> Email mmaguire at ebi.ac.uk >>>> >>>> >>>> >>>> >>>> ? ? ? ?[[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 >>> >>> -- >>> >>> >>> Wolfgang Huber >>> EMBL >>> http://www.embl.de/research/units/genome_biology/huber >>> >>> _______________________________________________ >>> 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 >>> > >> Michael Maguire >> Variation Archive Bioinformatician >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD >> >> Phone +44 1223 494674 >> Email mmaguire at ebi.ac.uk > > > >