au.csiro.variantspark.cli.PairWiseDistanceCmd.scala Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of variant-spark_2.11 Show documentation
Genomic variants interpretation toolkit
The newest version!
package au.csiro.variantspark.cli

import java.io.File

import scala.Range

import org.apache.commons.lang3.builder.ToStringBuilder
import au.csiro.pbdava.ssparkle.common.utils.Logging
import org.apache.spark.annotation.Private
import org.kohsuke.args4j.Option

import au.csiro.pbdava.ssparkle.common.arg4j.AppRunner
import au.csiro.pbdava.ssparkle.common.arg4j.TestArgs
import au.csiro.pbdava.ssparkle.common.utils.LoanUtils
import au.csiro.sparkle.common.args4j.ArgsApp
import au.csiro.variantspark.algo.PairwiseOperation
import au.csiro.variantspark.cli.args.FeatureSourceArgs
import au.csiro.variantspark.algo.PairwiseOperation
import au.csiro.variantspark.algo.metrics.EuclideanPairwiseMetric
import au.csiro.variantspark.algo.metrics.ManhattanPairwiseMetric
import au.csiro.variantspark.algo.metrics.BitwiseAndPairwiseRevMetric
import au.csiro.variantspark.algo.metrics.MultiPairwiseRevMetric
import au.csiro.variantspark.algo.metrics.SharedAltAlleleCount
import au.csiro.variantspark.algo.metrics.AtLeastOneSharedAltAlleleCount
import au.csiro.pbdava.ssparkle.common.utils.CSVUtils
import au.csiro.variantspark.input._

class PairWiseDistanceCmd extends ArgsApp with FeatureSourceArgs with Logging with TestArgs {

  @Option(name = "-of", required = true, usage = "Path to output distance file",
    aliases = Array("--output-file"))
  val outputFile: String = null

  @Option(name = "-m", required = false,
    usage = "Metric to use, one of: euclidean, manhattan, invBitAnd, invMul",
    aliases = Array("--metric"))
  val metricName: String = "euclidean"

  override def testArgs: Array[String] =
    Array("-if", "data/chr22_1000.vcf", "-of", "target/ch22-disc.csv", "-v", "-m", "manhattan")

  def buildMetricFromName(metricName: String): PairwiseOperation = {
    metricName match {
      case "euclidean" => EuclideanPairwiseMetric
      case "manhattan" => ManhattanPairwiseMetric
      case "invBitAnd" => BitwiseAndPairwiseRevMetric
      case "invMul" => MultiPairwiseRevMetric
      case "sharedAltCount" => SharedAltAlleleCount
      case "anySharedAltCount" => AtLeastOneSharedAltAlleleCount
      case _ => throw new IllegalArgumentException(metricName)
    }
  }

  override def run(): Unit = {
    logInfo("Running with params: " + ToStringBuilder.reflectionToString(this))
    val metric = buildMetricFromName(metricName)
    echo(s"Calculating pair wise distance: ${metric}")
    val data = featureSource.features.map(_.valueAsByteArray)
    echoDataPreview()
    val noOfSamples = data.first.length
    val resultAsMatrix = metric.compute(data).toMatrix
    val sampleNames = featureSource.sampleNames
    CSVUtils.withFile(new File(outputFile)) { writer =>
      writer.writeRow("" :: sampleNames)
      // since the matrix is symmetric does not matter that we output columns as rows
      Range(0, noOfSamples)
        .foreach(i => writer.writeRow(sampleNames(i) :: resultAsMatrix(::, i).toArray.toList))
    }
  }
}

object PairWiseDistanceCmd {
  def main(args: Array[String]) {
    AppRunner.mains[PairWiseDistanceCmd](args)
  }
}