hello BioC-users,

I would like to ask your hep in converting a data.frame for the use of
biomaRt.

I have a tab-delimited table of of protein ids that looks like that (this
is a part of a huge table from a proteomics experiment):

45  FBpp0070037
46  FBpp0070039;FBpp0070040
47  FBpp0070041;FBpp0070042;FBpp0070043
48  FBpp0070044;FBpp0110571
...

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","flybasename_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.

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