example of calling blast from ammonite

blast.sc

/// ceremony begins

import ammonite.ops._
import ammonite.ops.ImplicitWd._

import scala.util.Random


/// now we can write our script

println("Making random library")

val library = randomLibrary(10, 20, new Random())

val libraryAsfasta = library map (formatFasta _)

val libraryFile = "library.fa"

write.over(pwd/libraryFile, libraryAsfasta.mkString("\n"))


println("Running formatdb")

val dbName = "rand"

%(root / 'usr / 'bin / 'formatdb, "-t", "Random sequences", "-i", libraryFile, "-p", "F", "-n", dbName)

println("Running blast")

val blastFile = "blastResult"

%(root / 'usr / 'bin / 'blastn, "-db", dbName, "-query", libraryFile, "-out", blastFile )

println("Done")


/// helper types and functions

case class FastaSeq(descrTxt: String, seq: String)


def randomLibrary(size: Int, length: Int, rand: Random) =
  for(i <- 1 to size) yield
    FastaSeq(s"randseq_$i}",
             randomDna(length, rand))

def randomDna(length: Int, rand: Random): String = {
  val nucs = for(_ <- 0 until length) yield randomN(rand)
  nucs.mkString
}

def randomN(rand: Random): Char = rand.nextInt(4) match {
  case 0 => 'a'
  case 1 => 'g'
  case 2 =>'c'
  case 3 => 't'
}

def formatFasta(s: FastaSeq) =
  s""">${s.descrTxt}
     |${s.seq.grouped(60).mkString("\n")}""".stripMargin