Scala receipes

receipes.scala

/**
 * Return a Map[String,Any] of the field -> value pairs of the attributes of a class `c`.
 */
def classToMap(c: AnyRef): Map[String, Any] =
  // 'fold' syntax, starting with an empty map
  (Map[String, Any]() /: c.getClass.getDeclaredFields) {(a, f) =>
  f.setAccessible(true)
  a + (f.getName -> f.get(c))
}

/**
 * Return the value associated to class field `fieldName` given as a String.
 */
def getValue(c: AnyRef, fieldName: String) = {
  val vals = c.getClass.getDeclaredFields
    .filter { f: Field =>
      f.getName == fieldName
    } map { f: Field =>
      f.setAccessible(true)
      f.get(c)
    }
  vals.head
}

/*
 * Delete all files older than 1 hours in THAT_DIR with a given extension
 * Useful ref: http://alvinalexander.com/scala/how-to-list-files-in-directory-filter-names-scala
 */
// Get current time in milliseconds from 1970
import java.io.File
import java.util.Calendar
val now:Date = Calendar.getInstance().getTime
val millis = now.getTime  // yeah, getTime again...
val delta = 1 * 3600 * 1000 // 1h
new File(THAT_DIR).listFiles
  .filter(_.isFile)
  .filter(_.getName.matches(".*?\\.bam.*"))
  .filter(_.lastModified < now - delta).foreach(_.delete)
  
/* 
 * Create a random string
 */
import scala.util.Random
(Random.alphanumeric take 20).mkString 

/*
 * Read a JDBC database
 */
db.withConnection { conn =>	
	val cursor = conn.createStatement
	val res = cursor.executeQuery("SELECT ....")
	while (res.next()) {  ...  }
}

/*
 * Read (chr,start,end) from a BAM file with htsjdk
 */
import htsjdk.samtools.{SamReader, SamReaderFactory}
val reader: SamReader = SamReaderFactory.makeDefault().open(new File(filename))
val it = reader.iterator
while (it.hasNext) {
  val read = it.next
  println(read.getReferenceName, read.getAlignmentStart, read.getAlignmentEnd)
}
  
/*
 * Execute command-line
 * Useful ref: http://alvinalexander.com/scala/scala-execute-exec-external-system-commands-in-scala
 */
// Redirect stdout to file. Return the command's return code (0 = success)
val cmd = s"samtools view -hb $bam"  #>> new File(dest)
val success = cmd.! == 0
// Pipe. Return the stdout
val cmd = s"samtools view -hb $bam" #| "base64"
val encoded:String = cmd.!!