Updated phasing pipeline to properly read samples from VCF and BAM files
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5172 348d0f76-0448-11de-a6fe-93d51630548a
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@ -96,7 +96,9 @@ public class PhasingEval extends RodWalker<Integer, Integer> {
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int homalt = vc.getHomVarCount();
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int het = vc.getHetCount();
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int ac = 2 * homalt + het;
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//int an = 2 * (homref + homalt + het);
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PhasingByAC data = phasingByACs.get(ac);
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data.nHets += het > 0 ? 1 : 0;
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data.nHetsPhased += isPhysicallyPhased(vc.getGenotypes().values()) ? 1 : 0;
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@ -125,10 +127,10 @@ public class PhasingEval extends RodWalker<Integer, Integer> {
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public void onTraversalDone(Integer sum) {
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if (analysis == Analysis.PHASING_BY_AC) {
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out.println(Utils.join("\t", Arrays.asList("ac", "nhets", "nhetphased")));
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out.println(Utils.join("\t", Arrays.asList("ac", "an", "nhets", "nhetphased")));
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for (PhasingByAC pac : phasingByACs) {
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out.printf("%d\t%d\t%d%n", pac.myAC, pac.nHets, pac.nHetsPhased);
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out.printf("%d\t%d\t%d\t%d%n", pac.myAC, pac.myAN, pac.nHets, pac.nHetsPhased);
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}
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}
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}
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}
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}
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@ -2,41 +2,39 @@ import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
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import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
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import org.broadinstitute.sting.queue.QScript
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import org.apache.commons.io.FilenameUtils;
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import org.apache.commons.io.FilenameUtils
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import tools.nsc.io.Process;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType
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import scala.io.Source._
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class PhaseSamples extends QScript {
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qscript =>
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@Input(doc="bam input, as .bam or as a list of files", shortName="I", required=true)
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qscript =>
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@Input(doc = "bam input, as .bam or as a list of files", shortName = "I", required = true)
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var bams: File = _
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@Input(doc="master VCF calls", shortName="C", required=true)
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@Input(doc = "master VCF calls", shortName = "C", required = true)
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var masterCalls: File = _
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@Input(doc="file containing samples to be phased, as many as you like per line", shortName="samples", required=true)
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var samplesFile: File = _
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@Argument(doc="gatk jar file", shortName="J", required=true)
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@Argument(doc = "gatk jar file", shortName = "J", required = true)
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var gatkJarFile: File = _
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@Argument(shortName = "R", doc="ref", required=true)
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@Argument(shortName = "R", doc = "ref", required = true)
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var referenceFile: File = _
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@Argument(fullName = "prefix", doc="Prefix argument", required=false)
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@Argument(fullName = "prefix", doc = "Prefix argument", required = false)
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var prefix: String = ""
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@Argument(shortName = "L", doc="Intervals", required=false)
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@Argument(shortName = "L", doc = "Intervals", required = false)
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var intervals: String = _
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@Input(doc="level of parallelism for BAM phaser. By default is set to 0 [no scattering].", shortName="scatter", required=false)
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@Input(doc = "level of parallelism for BAM phaser. By default is set to 0 [no scattering].", shortName = "scatter", required = false)
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var scatterCount = 0
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@Input(doc="Samples to phase together. By default is set to 1 [one job per sample].", shortName="samplesPerJob", required=false)
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@Input(doc = "Samples to phase together. By default is set to 1 [one job per sample].", shortName = "samplesPerJob", required = false)
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var samplesPerJob = 1
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@Input(doc="Phased file to output", shortName="o", required=true)
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@Input(doc = "Phased file to output", shortName = "o", required = true)
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var outputPhased: File = _
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trait CommandLineGATKArgs extends CommandLineGATK {
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@ -47,93 +45,103 @@ class PhaseSamples extends QScript {
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this.logging_level = "INFO"
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}
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// A target has a list of samples and bam files to use for phasing
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class Target(val name: String, val samples: List[String], val bams: List[File]) {
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// A target has a list of samples and bam files to use for phasing
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class Target(val name: String, val samples: List[String], val bams: List[File]) {
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def phasedVCFFile = new File(name + "." + outputPhased)
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override def toString(): String = String.format("[Target %s with samples %s against bams %s]", name, samples, bams)
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}
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}
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def script = {
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if ( qscript.scatterCount > 0 ) throw new RuntimeException("scatter/gather currently not implemented")
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def script = {
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if (qscript.scatterCount > 0) throw new RuntimeException("scatter/gather currently not implemented")
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val samples: List[String] = getSamples(samplesFile)
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val samples: List[String] = getSamples()
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Console.out.printf("Samples are %s%n", samples)
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val targets: List[Target] = bamsToTargets(samples, bams)
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for (target <- targets) {
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Console.out.printf("Target is %s%n", target)
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add(new PhaseSamples(target))
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Console.out.printf("Target is %s%n", target)
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add(new PhaseSamples(target))
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}
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add(new CombineVariants(targets.map(_.phasedVCFFile)))
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}
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def bamsToTargets(samples: List[String], bamsIn: File): List[Target] = {
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add(new PhasingByACeval())
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}
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def bamsToTargets(samples: List[String], bamsIn: File): List[Target] = {
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val bams: List[File] = parseBamsInput(bamsIn)
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val sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]] = getMapOfBamsForSample(bams)
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def buildTargets(samples: List[String], count: Int): List[Target] = (samples splitAt samplesPerJob) match {
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case (Nil, y) =>
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return Nil
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case (subsamples, remaining) =>
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return new Target("group" + count, subsamples, findBamsForSamples(subsamples, bams)) ::
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buildTargets(remaining, count + 1)
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case (Nil, y) =>
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return Nil
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case (subsamples, remaining) =>
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return new Target("group" + count, subsamples, findBamsForSamples(subsamples, sampleToBams)) ::
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buildTargets(remaining, count + 1)
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}
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return buildTargets(samples, 0)
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}
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}
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// determines the bam files to use for these samples. If there's only a single bam, assumes this file
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// is a merge of all sample bams. If there are multiple bams, for each sample, finds all bam files
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// containing sample in their path (should really check header?). The phasing bams are the merge of
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// these files
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def findBamsForSamples( samples: List[String], bams: List[File] ): List[File] = bams match {
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case x :: Nil => return bams
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case _ =>
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return findBamsForSamplesHelper(samples, bams)
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}
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def getMapOfBamsForSample(bams: List[File]): scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]] = bams match {
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case Nil => return scala.collection.mutable.Map.empty[String, scala.collection.mutable.Set[File]]
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def findBamsForSamplesHelper( samples: List[String], bams: List[File] ): List[File] = bams match {
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case Nil => Nil
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case x :: y =>
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val line: File = matchSamplesInSingleBam(x, samples)
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val restOfList: List[File] = findBamsForSamplesHelper(samples, y)
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if (line != null)
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line :: restOfList
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else
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restOfList
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}
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val m: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]] = getMapOfBamsForSample(y)
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// If the line (bam file name) contains ANY sample match, we use it:
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def matchSamplesInSingleBam( line : File, samples: List[String] ) : File = samples match {
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case Nil => null
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case x :: y => if (line.getName().contains(x)) line else matchSamplesInSingleBam(line, y)
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}
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val getBamSamplesCommand: String = "samtools view -H " + x.getPath() + " | grep '^@RG' | awk '{for (i = 1; i <= NF; i++) if (substr($i,1,3) == \"SM:\") print substr($i,4)}' | sort | uniq"
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//println("getBamSamplesCommand: " + getBamSamplesCommand)
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val bamSamples: List[String] = Process(getBamSamplesCommand).iterator toList
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// todo -- allow us to get the master list of samples from the VCF for convenience
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def getSamples(samplesFile: File): List[String] = {
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return (for { line <- fromFile(samplesFile).getLines
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part <- line.split("\\s", 0).iterator }
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yield part ).toList
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}
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for (s <- bamSamples) {
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if (!m.contains(s))
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m += s -> scala.collection.mutable.Set.empty[File]
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def parseBamsInput(bamsIn: File): List[File] = FilenameUtils.getExtension(bamsIn.getPath) match {
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m(s) = m(s) + x
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}
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return m
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}
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def findBamsForSamples(samples: List[String], sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]]): List[File] = {
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val l: List[File] = Nil
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l ++ findBamsForSamplesHelper(samples, sampleToBams)
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}
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def findBamsForSamplesHelper(samples: List[String], sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]]): scala.collection.mutable.Set[File] = samples match {
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case Nil => scala.collection.mutable.Set.empty[File]
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case x :: y =>
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var bamsForSampleX: scala.collection.mutable.Set[File] = scala.collection.mutable.Set.empty[File]
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if (sampleToBams.contains(x))
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bamsForSampleX = sampleToBams(x)
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return bamsForSampleX ++ findBamsForSamplesHelper(y, sampleToBams)
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}
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def getSamples(): List[String] = {
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val getSamplesCommand: String = "cat " + masterCalls.getPath() + " | grep '^#CHROM' | head -1 | awk '{for (i = 10; i <= NF; i++) print $i}'"
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//println("getSamplesCommand: " + getSamplesCommand)
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return Process(getSamplesCommand).iterator toList
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}
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def parseBamsInput(bamsIn: File): List[File] = FilenameUtils.getExtension(bamsIn.getPath) match {
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case "bam" => return List(bamsIn)
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case "list" => return (for( line <- fromFile(bamsIn).getLines) yield new File(line)).toList
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case "list" => return (for (line <- fromFile(bamsIn).getLines) yield new File(line)).toList
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case _ => throw new RuntimeException("Unexpected BAM input type: " + bamsIn + "; only permitted extensions are .bam and .list")
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}
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}
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class PhaseSamples(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.ReadBackedPhasing with CommandLineGATKArgs {
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class PhaseSamples(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.ReadBackedPhasing with CommandLineGATKArgs {
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this.rodBind :+= RodBind("variant", "VCF", qscript.masterCalls)
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this.out = t.phasedVCFFile
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this.input_file = t.bams
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this.sampleToPhase = t.samples
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}
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}
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class CombineVariants(vcfsToCombine: List[File]) extends org.broadinstitute.sting.queue.extensions.gatk.CombineVariants with CommandLineGATKArgs {
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for ( vcf <- vcfsToCombine ) {
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this.rodBind :+= RodBind(vcf.getName, "VCF", vcf)
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class CombineVariants(vcfsToCombine: List[File]) extends org.broadinstitute.sting.queue.extensions.gatk.CombineVariants with CommandLineGATKArgs {
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for (vcf <- vcfsToCombine) {
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this.rodBind :+= RodBind(vcf.getName, "VCF", vcf)
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}
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// add the master call:
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@ -141,6 +149,12 @@ class CombineVariants(vcfsToCombine: List[File]) extends org.broadinstitute.stin
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this.variantMergeOptions = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.MASTER)
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this.out = outputPhased
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}
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}
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}
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class PhasingByACeval() extends org.broadinstitute.sting.queue.extensions.gatk.PhasingEval with CommandLineGATKArgs {
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this.analysis = org.broadinstitute.sting.oneoffprojects.walkers.phasing.PhasingEval.Analysis.PHASING_BY_AC
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this.out = new File("phasing_by_ac." + outputPhased + ".txt")
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}
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}
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