##Get input and output from command line
args <- commandArgs(TRUE)
inputfilename=args[1]
outputfilename=args[2]


blastdata<-read.table(inputfilename)

output<-data.frame()

for (query in levels(blastdata[,1]) ){

	##Build querylist containing all results for this query
	indexes<-which(blastdata[,1]==query)
	querylist<-blastdata[indexes,]

	##Find best match (minimum evalue)
	##Note: E value is column number 13
	bestmatchindex=which.min(querylist[,13])

	##Add best match line to dataframe of outputs
	output=rbind(output,querylist[bestmatchindex,])
}


write.table(output,file=outputfilename,sep="\t",quote=FALSE,row.names=FALSE,col.names=FALSE)