au.csiro.variantspark.output.CSVFeatureSink.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.output

import au.csiro.variantspark.input.FeatureSource
import java.io.FileWriter
import au.csiro.pbdava.ssparkle.common.utils.CSVUtils
import java.io.File

/**
  * This only works for smallish datasets (used local files)
  */
case class CSVFeatureSink(fileName: String) extends FeatureSink {

  def save(fs: FeatureSource) {
    CSVUtils.withFile(new File(fileName)) { csvWriter =>
      csvWriter.writeRow("" :: fs.sampleNames)
      csvWriter.writeAll(fs.features.collect().toSeq.map(f => f.label :: f.valueAsStrings))
    }
  }

}