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

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package au.csiro.variantspark.cli

import au.csiro.sparkle.common.args4j.ArgsApp
import au.csiro.sparkle.cmd.CmdApp
import org.kohsuke.args4j.Option
import au.csiro.pbdava.ssparkle.common.arg4j.AppRunner
import au.csiro.pbdava.ssparkle.spark.SparkApp
import collection.JavaConverters._
import au.csiro.variantspark.input.VCFSource
import au.csiro.variantspark.input.VCFFeatureSource
import au.csiro.variantspark.input.HashingLabelSource
import org.apache.spark.mllib.linalg.Vectors
import au.csiro.variantspark.input.CsvLabelSource
import au.csiro.variantspark.cmd.Echoable
import au.csiro.pbdava.ssparkle.common.utils.Logging
import org.apache.commons.lang3.builder.ToStringBuilder
import au.csiro.variantspark.cmd.EchoUtils._
import au.csiro.pbdava.ssparkle.common.utils.LoanUtils
import au.csiro.pbdava.ssparkle.common.arg4j.TestArgs
import org.apache.hadoop.fs.FileSystem
import org.apache.commons.math3.stat.correlation.PearsonsCorrelation
import au.csiro.pbdava.ssparkle.spark.SparkUtils
import au.csiro.pbdava.ssparkle.common.utils.ReusablePrintStream
import au.csiro.variantspark.algo.RandomForestCallback
import au.csiro.variantspark.utils.VectorRDDFunction._
import au.csiro.variantspark.input.CsvFeatureSource
import au.csiro.variantspark.algo.RandomForestParams
import au.csiro.variantspark.data.BoundedOrdinalVariable
import au.csiro.pbdava.ssparkle.common.utils.Timer
import au.csiro.variantspark.utils.defRng
import au.csiro.variantspark.input.generate.OrdinalFeatureGenerator
import au.csiro.variantspark.output.CSVFeatureSink
import au.csiro.variantspark.input.ParquetFeatureSource
import au.csiro.variantspark.input.generate.EffectLabelGenerator
import java.io.File
import java.util.ArrayList
import au.csiro.variantspark.cli.args.FeatureSourceArgs
import au.csiro.variantspark.output.CSVFeatureSink2

class ConvertCmd extends ArgsApp with FeatureSourceArgs with Echoable with Logging with TestArgs {

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

  @Option(name = "-ot", required = false, usage = "Input file type, one of: vcf, csv (def=vcf)",
    aliases = Array("--output-type"))
  val outputType: String = null

  override def testArgs: Array[String] =
    Array("-if", "data/chr22_1000.vcf", "-it", "vcf", "-sp", "4", "-of", "target/getds.csv")

  override def run(): Unit = {
    logInfo("Running with params: " + ToStringBuilder.reflectionToString(this))

    echo(s"Converting from: ${inputType} to: ${outputType}")

    echo(s"Loading parquet file: ${inputFile}")
    echo(s"Loaded rows: ${dumpList(featureSource.sampleNames)}")

    val sink = CSVFeatureSink2(outputFile)
    sink.save(featureSource)
  }
}

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