Response to http://www.reddit.com/r/scala/comments/2u3o66/thinking_in_scala/

fasta.txt

> Fake Line
AGCTACGACTAGCCGCGCGCTATATACTAGCATCGACATTTTTATATTAAGACGAGACTATCATATACTAGCGAGCGCGGCACTATATTTGCTCGACTACACAGCCATCAAGATCAACACATATATACTTCCCCTATACACCAACACAGCGGGGACGAATACTATCATCATCATCATCAGCGCGCGCGCAGCAGAGGAAGGAAGGAATTCCTCTACTCTATTTATAGACGCGASAGCAG
> New Line
AGTAGAT
> Cat
> Doghead
AGTCG
GAT
GGG
C
GAGTCAG
> Noodles
G

FastaTestMain.scala

import scala.io.Source

object FastaTestMain {
  
  val header = """^>\s*(.*?)\s*$""".r // Allows destructuring pattern match in parse()
  
  case class FastaItem(header: String, sequence: String)
  
  def readFile(filename: String): Iterator[FastaItem] = {
    val conditioned = Source.fromFile("fasta.txt").getLines.map(_.trim).filter(_ != "") // Trim and skip blank lines
    val start: (Option[String], Option[String]) = (None, None) // Tuple: At start, no header (left) and no sequence (right)
    val parsed = conditioned.scanLeft(start) { case x@(state, line) => x match {
        case (_, header(h)) => (Some(h), None) // If we see a header, remember it in the state going forward
        case ((ho, _), s) => (ho, Some(s)) // If we see a sequence, associate it to the remembered header from the state
      }
    }
    for {
      (ho, so) <- parsed // Iterate over the pairs of optional header and optional sequence
      h <- ho // Only keep the pair if it has a header
      s <- so // Only keep the pair if it has a sequence
    } yield FastaItem(h, s)
  }
  
  def main(args: Array[String]): Unit = {
    for (i <- readFile("fasta.txt")) {
      println(i)
    }
  }
  
}