R/BlastN.R

In johnathanlo/chromPaintR: In-Silico Chromosome Painting

library(Rcpp)
#sourceCpp("FastaSlice_ver04.cpp")

BlastN <- function(query, db, slicesize=100, leaps=900){
  if (file.exists(query) && file.exists(db)&&slicesize>10){
  x <- FastaSlice(query, db, slicesize, leaps)
  }else if(!file.exists(query) || !file.exists(db)) {
    print("File does not exist. ")
  }else{
    print("Slicesize must be greater than 10")
  }
  #write(query, file = "query/query.fsa")
  #syscommand <- paste("blastn -db ", target, " -query query/query.fsa -outfmt '6 qseqid sseqid length pident score' -out rtest.out", sep = "")
  #system(syscommand)
}