zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added queue/util/BAMutilities Object [with BAM and VCF parsing utilities], which is now used by my qscripts that robustly split runs by sample 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5214 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2011-02-07 22:17:29 +00:00
parent 8040998c15
commit 8d0f1b75d5
3 changed files with 102 additions and 64 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

64
scala/qscript/oneoffs/fromer/PhaseSamples.scala
View File

@ -1,11 +1,8 @@
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
package oneoffs.fromer
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
import org.broadinstitute.sting.queue.QScript
import org.apache.commons.io.FilenameUtils
import tools.nsc.io.Process;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType
import scala.io.Source._
import org.broadinstitute.sting.queue.util.BAMutilities
class PhaseSamples extends QScript {
qscript =>
@ -55,7 +52,7 @@ class PhaseSamples extends QScript {
def script = {
if (qscript.scatterCount > 0) throw new RuntimeException("scatter/gather currently not implemented")
val samples: List[String] = getSamples()
val samples: List[String] = BAMutilities.getSamplesFromVCF(masterCalls)
Console.out.printf("Samples are %s%n", samples)
val targets: List[Target] = bamsToTargets(samples, bams)
@ -71,67 +68,20 @@ class PhaseSamples extends QScript {
}
def bamsToTargets(samples: List[String], bamsIn: File): List[Target] = {
val bams: List[File] = parseBamsInput(bamsIn)
val sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]] = getMapOfBamsForSample(bams)
val bams: List[File] = BAMutilities.parseBamsInput(bamsIn)
val sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]] = BAMutilities.getMapOfBamsForSample(bams)
def buildTargets(samples: List[String], count: Int): List[Target] = (samples splitAt samplesPerJob) match {
case (Nil, y) =>
return Nil
case (subsamples, remaining) =>
return new Target("group" + count, subsamples, findBamsForSamples(subsamples, sampleToBams)) ::
return new Target("group" + count, subsamples, BAMutilities.findBamsForSamples(subsamples, sampleToBams)) ::
buildTargets(remaining, count + 1)
}
return buildTargets(samples, 0)
}
def getMapOfBamsForSample(bams: List[File]): scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]] = bams match {
case Nil => return scala.collection.mutable.Map.empty[String, scala.collection.mutable.Set[File]]
case x :: y =>
val m: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]] = getMapOfBamsForSample(y)
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"
//println("getBamSamplesCommand: " + getBamSamplesCommand)
val bamSamples: List[String] = Process(getBamSamplesCommand).iterator toList
for (s <- bamSamples) {
if (!m.contains(s))
m += s -> scala.collection.mutable.Set.empty[File]
m(s) = m(s) + x
}
return m
}
def findBamsForSamples(samples: List[String], sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]]): List[File] = {
val l: List[File] = Nil
l ++ findBamsForSamplesHelper(samples, sampleToBams)
}
def findBamsForSamplesHelper(samples: List[String], sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]]): scala.collection.mutable.Set[File] = samples match {
case Nil => scala.collection.mutable.Set.empty[File]
case x :: y =>
var bamsForSampleX: scala.collection.mutable.Set[File] = scala.collection.mutable.Set.empty[File]
if (sampleToBams.contains(x))
bamsForSampleX = sampleToBams(x)
return bamsForSampleX ++ findBamsForSamplesHelper(y, sampleToBams)
}
def getSamples(): List[String] = {
val getSamplesCommand: String = "cat " + masterCalls.getPath() + " | grep '^#CHROM' | head -1 | awk '{for (i = 10; i <= NF; i++) print $i}'"
//println("getSamplesCommand: " + getSamplesCommand)
return Process(getSamplesCommand).iterator toList
}
def parseBamsInput(bamsIn: File): List[File] = FilenameUtils.getExtension(bamsIn.getPath) match {
case "bam" => return List(bamsIn)
case "list" => return (for (line <- fromFile(bamsIn).getLines) yield new File(line)).toList
case _ => throw new RuntimeException("Unexpected BAM input type: " + bamsIn + "; only permitted extensions are .bam and .list")
}
class PhaseSamples(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.ReadBackedPhasing with CommandLineGATKArgs {
this.rodBind :+= RodBind("variant", "VCF", qscript.masterCalls)
this.out = t.phasedVCFFile

46
scala/qscript/oneoffs/fromer/ReadDepthCNVanalysis.scala
View File

@ -2,8 +2,8 @@ package oneoffs.fromer
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.gatk.DownsampleType
import org.broadinstitute.sting.queue.util.BAMutilities
class ReadDepthCNVanalysis extends QScript {
@ -24,6 +24,9 @@ class ReadDepthCNVanalysis extends QScript {
@Input(doc = "level of parallelism for BAM DoC. By default is set to 0 [no scattering].", shortName = "scatter", required = false)
var scatterCountInput = 0
@Input(doc = "Samples to phase together. By default is set to 1 [one job per sample].", shortName = "samplesPerJob", required = false)
var samplesPerJob = 1
@Output(doc = "DoC file to output", shortName = "o", required = true)
var outputDoC: File = _
@ -44,11 +47,40 @@ class ReadDepthCNVanalysis extends QScript {
this.logging_level = "INFO"
}
def script = {
add(new DepthOfCoverage(bams, outputDoC))
// A target has a list of samples and bam files to use for DoC
class Target(val name: String, val samples: List[String], val bams: List[File]) {
def DoC_output = new File(name + "." + outputDoC)
override def toString(): String = String.format("[Target %s with samples %s against bams %s]", name, samples, bams)
}
class DepthOfCoverage(bam: File, docOutPath: File) extends org.broadinstitute.sting.queue.extensions.gatk.DepthOfCoverage with CommandLineGATKArgs {
def script = {
val sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]] = BAMutilities.getMapOfBamsForSample(BAMutilities.parseBamsInput(bams))
val samples: List[String] = sampleToBams.keys.toList
Console.out.printf("Samples are %s%n", samples)
val targets: List[Target] = buildTargets(samples, sampleToBams)
for (target <- targets) {
Console.out.printf("Target is %s%n", target)
add(new DoC(target))
}
}
def buildTargets(samples: List[String], sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]]): List[Target] = {
def buildTargetsHelper(samples: List[String], count: Int): List[Target] = (samples splitAt samplesPerJob) match {
case (Nil, y) =>
return Nil
case (subsamples, remaining) =>
return new Target("group" + count, subsamples, BAMutilities.findBamsForSamples(subsamples, sampleToBams)) ::
buildTargetsHelper(remaining, count + 1)
}
return buildTargetsHelper(samples, 0)
}
class DoC(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.DepthOfCoverage with CommandLineGATKArgs {
this.omitIntervalStatistics = false
this.omitDepthOutputAtEachBase = true
this.omitLocusTable = true
@ -56,8 +88,8 @@ class ReadDepthCNVanalysis extends QScript {
this.minBaseQuality = Some(0)
this.minMappingQuality = Some(0)
this.out = docOutPath
this.input_file :+= bam
this.out = t.DoC_output
this.input_file = t.bams
this.dcov = Some(MAX_DEPTH)
this.downsampling_type = Some(DownsampleType.BY_SAMPLE)
@ -68,7 +100,7 @@ class ReadDepthCNVanalysis extends QScript {
this.scatterCount = scatterCountInput
override def dotString = "DOC: " + bam.getName
override def dotString = "DOC: " + t.DoC_output
}
}

56
scala/src/org/broadinstitute/sting/queue/util/BAMutilities.scala 100644
View File

@ -0,0 +1,56 @@
package org.broadinstitute.sting.queue.util
import tools.nsc.io.Process
import java.io.File
import org.apache.commons.io.FilenameUtils
import scala.io.Source._
object BAMutilities {
def getSamplesFromVCF(calls: File): List[String] = {
val getSamplesCommand: String = "cat " + calls.getPath() + " | grep '^#CHROM' | head -1 | awk '{for (i = 10; i <= NF; i++) print $i}'"
//println("getSamplesCommand: " + getSamplesCommand)
return Process(getSamplesCommand).iterator toList
}
def parseBamsInput(bamsIn: File): List[File] = FilenameUtils.getExtension(bamsIn.getPath) match {
case "bam" => return List(bamsIn)
case "list" => return (for (line <- fromFile(bamsIn).getLines) yield new File(line)).toList
case _ => throw new RuntimeException("Unexpected BAM input type: " + bamsIn + "; only permitted extensions are .bam and .list")
}
def getMapOfBamsForSample(bams: List[File]): scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]] = bams match {
case Nil => return scala.collection.mutable.Map.empty[String, scala.collection.mutable.Set[File]]
case x :: y =>
val m: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]] = getMapOfBamsForSample(y)
val getBamSamplesCommand: String = "samtools view -H " + x.getPath() + " | grep '^@RG' | awk '{for (i = 1; i <= NF; i++) if (substr($i,1,3) == \"SM:\") print substr($i,4)}' | sort | uniq"
//println("getBamSamplesCommand: " + getBamSamplesCommand)
val bamSamples: List[String] = Process(getBamSamplesCommand).iterator toList
for (s <- bamSamples) {
if (!m.contains(s))
m += s -> scala.collection.mutable.Set.empty[File]
m(s) = m(s) + x
}
return m
}
def findBamsForSamples(samples: List[String], sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]]): List[File] = {
val l: List[File] = Nil
l ++ findBamsForSamplesHelper(samples, sampleToBams)
}
def findBamsForSamplesHelper(samples: List[String], sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]]): scala.collection.mutable.Set[File] = samples match {
case Nil => scala.collection.mutable.Set.empty[File]
case x :: y =>
var bamsForSampleX: scala.collection.mutable.Set[File] = scala.collection.mutable.Set.empty[File]
if (sampleToBams.contains(x))
bamsForSampleX = sampleToBams(x)
return bamsForSampleX ++ findBamsForSamplesHelper(y, sampleToBams)
}
}