Hi all,

I'm currently trying to write a script allowing me to get some informations about several (actually about 18000 per file) sequence intervals. My query works, but I can't throw it all my file long.

Basically, I throw my request with getBM as many as my file got lines, but after a while, the connection cuts, and i have this error message :
Erreur dans postForm(paste(martHost(mart), "?", sep = ""), query = xmlQuery) : 
  couldn't connect to host

Is there a way to "test" the postForm method or the connection with biomaRt from R before throwing the request ?

Here is my script :


file="/myfile"

chr=9
db=useMart("ensembl")
ensembl=useDataset("hsapiens_gene_ensembl",mart=db)
filtres = c("chromosome_name","start","end")
attributs = c("ensembl_gene_id","embl","description","start_position","end_position")

data <- read.table(file, sep="\t", header=T)

query <- function (chr,start, end) {
     valeurs = list(chr, start, end)
    genes=getBM(mart=ensembl, filters=filtres,values=valeurs,attributes=attributs)
    martDisconnect(ensembl) 
}

genes=c()
    
for(i in 1:nrow(data)){

     genes=query(chr,data[i,1],data[i,2])    
    
}




Thanks for your help,

Marion



      
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