R/sendFA.R

In hoardeR: Collect and Retrieve Annotation Data for Various Genomic Data Using Different Webservices

sendFA <- function(FAseq, database, hl_size=20, program="blastn", filter="L", expect=10, email, method="PUT", logFolder, verbose){
 if(method=="PUT"){
   blastRun <- scan(paste("https://blast.ncbi.nlm.nih.gov/Blast.cgi?QUERY=",FAseq,"&DATABASE=",database,"&HITLIST_SIZE=",hl_size,"&FILTER=",filter,"&EXPECT=",expect,"&PROGRAM=",program,"&CLIENT=web&SERVICE=plain&NCBI_GI=on&PAGE=Nucleotides&CMD=Put&EMAIL=",email,"&TOOL=hoardeR" ,sep=""),what="raw")
   RIDNo <- which((blastRun=="RID")==TRUE)
   RIDNo <- blastRun[RIDNo+2]
 } else if(method=="POST"){  
   tries <- 0
   newError <- TRUE
   while(newError & tries < 6){
     newError <- FALSE
     sendThisBody <- list(QUERY=as.vector(FAseq),
                          DATABASE=database,
                          HITLIST_SIZE=hl_size,
                          FILTER=filter,
                          EXPECT=expect,
                          PROGRAM=program,
                          CLIENT="web",
                          SERVICE="plain",
                          NCBI_GI="on",
                          PAGE="Nucleotides",
                          CMD="Put",
                          EMAIL=email,
                          TOOL="R")
     if(verbose)print(sendThisBody)
     tryCatch(post <- POST(url="https://blast.ncbi.nlm.nih.gov/Blast.cgi",
                           body=sendThisBody,
                           verbose()
                   )
               , error = function(e){
                         cat("An error occured, try",tries,"\n")  
                         if(verbose) message(e)
                         Sys.sleep(10)
                         newError <<- TRUE
                         tries <<- tries + 1
                         }
             )
   }
   blastRun <- read.csv(text=rawToChar(post$content),header=T,sep="\t", stringsAsFactor=FALSE)
   if(verbose & !is.null(logFolder)){
     sink(file.path(logFolder,paste("ncbiReturn-sendFA-",date(),".html",sep="") ))
     print(blastRun)
     sink()
   }
   RIDNo <- blastRun[grepl("RID =",blastRun[,1]),1]
   RIDNo <- strsplit(RIDNo," = ")[[1]][2]
 }
 RIDNo
}