On 01/26/2012 01:24 AM, Hans-Rudolf Hotz wrote: > > > On 01/26/2012 08:28 AM, Assa Yeroslaviz wrote: >> Hi Steve, >> >> thanks for the help. >> >> I know about the strsplit function and i used it to split each row on its >> own by the ';' symbol. >> The problem I have is that I need to keep the information of each row in >> the row ( or at least to give it back after the biomaRt extraction). >> >> The table I have contains not only the protein IDs but also a lot of >> other >> stuff, which is connected to each of the proteins. This is why I need to >> know which proteins came from which line (Id). >> >> It will be nice if there was a possibility to do it as you suggested. >> Take >> all the Protein IDs, write them into one vector and run them with >> biomaRt. >> But than I would like to be able to put them back together in a row-wise >> fashion like I suggested at the beginning. >> > > Hi > > Please allow me to jump in: > > If I understand your question correctly, then there is no other (easy) > solution than querying biomart inside a loop. > > The problem is not the Bioconductor packagae biomaRt, but the actual > biomart server behind the scene: Apparently there is now way to preserve > the order of the input (or keep duplicates, or indicate which id does > not have a result, etc). If the original ids are in a data.frame df <- data.frame(FBpp=c("FBpp0070037", "FBpp0070039;FBpp0070040", "FBpp0070041;FBpp0070042;FBpp0070043", "FBpp0070044;FBpp0110571"), stringsAsFactors=FALSE) and the 'split' ids are ids <- strsplit(df$FBpp, ";") then 'map' relates the ids to the row they come from: map <- rep(seq_len(nrow(df)), sapply(ids, length)) names(map) <- unlist(ids) so after querying biomaRt library(biomaRt) mart <- useMart('ensembl', dataset='dmelanogaster_gene_ensembl') ans <- getBM(attributes=c("flybase_translation_id", "flybase_gene_id", "flybasename_gene"), filters="flybase_translation_id", values=names(map), mart=mart) and writing a little helper function to 'unsplit' a character vector x into 'collapsed' strings based on a factor f strunsplit <- function(x, f, collapse=";") { sapply(split(x, f), paste, collapse=collapse) } the original data.frame can be updated as FBgn <- strunsplit(ans$flybase_gene_id, map[ans$flybase_translation_id]) df$FBgn[as.integer(names(FBgn))] <- FBgn I guess the contortions occur because of the original data.frame. A different representation with the same information, assuming 'Id' is the criterion for joining the FBbb ids in the first place, is > df1 <- data.frame(Id=map, FBpp=names(map), row.names=NULL) > df1 Id FBpp 1 1 FBpp0070037 2 2 FBpp0070039 3 2 FBpp0070040 ... Martin > > I recently asked the biomart folks about this issue, and the answer was > that I need to post-process the output to get my original order back - I > was lazy, and I queried the server in a loop (for my defense: it was > only a handful of ids) > > > Regards, Hans > >> Thanks again >> Assa >> >> On Wed, Jan 25, 2012 at 16:02, Steve Lianoglou< >> mailinglist.honeypot at gmail.com> wrote: >> >>> Hi Assa, >>> >>> Sorry for top posting. >>> >>> Your intuition is correct: you should not being querying biomart >>> inside a for loop. The idea is to create one query for all of your >>> protein IDs, and query it once. >>> >>> This is how you might go about it. First, let's look at the protein >>> IDs you already seem to have somewhere: >>> >>>> 45 FBpp0070037 >>>> 46 FBpp0070039;FBpp0070040 >>>> 47 FBpp0070041;FBpp0070042;FBpp0070043 >>>> 48 FBpp0070044;FBpp0110571 >>> >>> It seems you have multiple IDs jammed into one column of a data.frame >>> maybe? The rows which have more than one ID, (eg. >>> "FBpp0070039;FBpp0070040") will have to be split up so that each row >>> (or element in a vector) only has one ID. Look into using `strsplit`. >>> >>> You will need to get a character vector of protein ids -- one protein >>> per bin, it might look like so: >>> >>> pids<- c('FBpp0070037', 'FBpp0070039', 'FBpp0070040', 'FBpp0070041', >>> 'FBpp0070042', 'FBpp0070043') >>> >>> Now ... you're basically done. Let's rig up an object to query biomart >>> with: >>> >>> library(biomaRt) >>> mart<- useMart('ensembl', dataset='dmelanogaster_gene_ensembl') >>> ans<- >>> getBM(attributes=c("flybase_translation_id","flybase_gene_id","fly basename_gene"), >>> >>> filters="flybase_translation_id", values=pids, >>> mart=mart) >>> >>> Your answer will look like so: >>> >>> flybase_translation_id flybase_gene_id flybasename_gene >>> 1 FBpp0070037 FBgn0010215 alpha-Cat >>> 2 FBpp0070039 FBgn0052230 CG32230 >>> 3 FBpp0070040 FBgn0052230 CG32230 >>> 4 FBpp0070041 FBgn0000258 CkIIalpha >>> 5 FBpp0070042 FBgn0000258 CkIIalpha >>> 6 FBpp0070043 FBgn0000258 CkIIalpha >>> >>> Now you're left with figuring out what to do with multiple >>> "flybase_translaion_id"s that map to the same "flybasename_gene". >>> >>> You would have to do this anyway, but the key point here is that you >>> can now do it without querying biomart in a loop. >>> >>> HTH, >>> -steve >>> >>> >>> >>>> For each of these protein Ids (FBpp...), I would like to extract the >>>> gene >>>> id (Fbgn....) in a third column. the output table should looks like >>>> that: >>>> >>>> 45 FBpp0070037 FBgn001234 >>>> 46 FBpp0070039;FBpp0070040 FBgn00094432;FBgn002345 >>>> 47 FBpp0070041;FBpp0070042;FBpp0070043 >>> FBgn0001936;FBgn000102;FBgn004527 >>>> 48 FBpp0070044;FBpp0110571 FBgn0097234;FBgn00183 >>>> ... >>>> >>>> I was thinking using biomaRt, but I could find a way of automating >>>> it for >>>> the complete protein ids in the line. >>>> >>>> What I have done so far is this for loop: >>>> >>>> for(i in 1:dim(data)[1]){ >>>> temp=unlist(strsplit(data[i,2],";")) >>>> temp= gsub("REV__", "", temp) >>>> result= >>>> >>> getBM(attributes=c("flybase_translation_id","flybase_gene_id","fly basename_gene"),filters="flybase_translation_id",values=temp, >>> >>>> mart=mart, ) >>>> charresult ="" >>>> for (j in 1:length(result[[1]])) { >>>> # charresult<-paste(charresult,">", >>>> result[[1]][j],":",result[[2]][j], "\t", sep="") >>>> charresult<-paste(charresult, result[[2]][j], ";", sep="") >>>> } >>>> out<-"CompleteResults.txt" >>>> cat("line: ", i-1,"\t", "was written to ");cat(out);cat("\n") >>>> write.table(paste(i-1, charresult, sep="\t"),out, sep="\t", quote=F, >>>> col.names=F, row.names=F,append=T) >>>> } >>>> >>>> What I am doing is converting the string of FBpp Ids into a character >>>> vector and than run each line into the getBM command. I first think it >>> is a >>>> bad idea, as I am using a loop to inquire an online data base, but i >>> don't >>>> have a better option at the moment. >>>> >>>> The second problem is that it just takes a lot of time. >>>> >>>> I would appreciate your Ideas, If there is a better/faster way of doing >>> it >>>> >>>> Thanks A. >>>> >>>> [[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 >>> >>> >>> >>> -- >>> Steve Lianoglou >>> Graduate Student: Computational Systems Biology >>> | Memorial Sloan-Kettering Cancer Center >>> | Weill Medical College of Cornell University >>> Contact Info: http://cbio.mskcc.org/~lianos/contact >>> >> >> [[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 > > _______________________________________________ > 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. 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