## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)

## ----setup--------------------------------------------------------------------
library("rBLAST")

## ----include = FALSE----------------------------------------------------------
# only run code if blast+ is installed
run <- has_blast()

## ----echo = FALSE, eval = !run, results='asis'--------------------------------
cat("**Note: BLAST was not installed when this vignette was built. Some output is not available in this vignette!**")

## ----eval=run-----------------------------------------------------------------
#  Sys.which("blastn")

## ----eval=run-----------------------------------------------------------------
#  Sys.setenv(PATH = paste(Sys.getenv("PATH"),
#     "path_to_your_BLAST_installation", sep=.Platform$path.sep))

## ----eval=run-----------------------------------------------------------------
#  ## download the 16S Microbial rRNA data base from NCBI
#  tgz_file <- blast_db_get("16S_ribosomal_RNA.tar.gz")
#  untar(tgz_file, exdir = "16S_rRNA_DB")

## ----eval=run-----------------------------------------------------------------
#  list.files("./16S_rRNA_DB/")

## ----eval=run-----------------------------------------------------------------
#  bl <- blast(db = "./16S_rRNA_DB/16S_ribosomal_RNA")
#  bl

## ----eval=run-----------------------------------------------------------------
#  seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
#      package = "rBLAST"
#  ))[1]
#  seq
#  
#  cl <- predict(bl, seq)
#  nrow(cl)
#  cl[1:5, ]

## ----eval=run-----------------------------------------------------------------
#  fmt <- paste(
#      "qaccver saccver pident length mismatch gapopen qstart qend",
#      "sstart send evalue bitscore qseq sseq"
#  )
#  cl <- predict(bl, seq,
#      BLAST_args = "-perc_identity 99",
#      custom_format = fmt
#  )
#  cl

## ----include = FALSE, eval=run------------------------------------------------
#  ## clean up
#  unlink("16S_rRNA_DB", recursive = TRUE)

## -----------------------------------------------------------------------------
seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
    package = "rBLAST"
))
seq

## -----------------------------------------------------------------------------
writeXStringSet(seq, filepath = "seqs.fasta")

## ----eval=run-----------------------------------------------------------------
#  makeblastdb("seqs.fasta", db_name = "db/small", dbtype = "nucl")

## ----eval=run-----------------------------------------------------------------
#  db <- blast("db/small")
#  db

## ----eval=run-----------------------------------------------------------------
#  fragment <- subseq(seq[1], start = 101, end = 200)
#  fragment
#  
#  predict(db, fragment)

## -----------------------------------------------------------------------------
unlink("seqs.fasta")
unlink("db", recursive = TRUE)

## -----------------------------------------------------------------------------
sessionInfo()