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Commit 3a0b6423 authored by bow's avatar bow
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Merge branch 'feature-toolcommands' into 'develop' 

Feature toolcommands

Added 4 tools from Sage
see also #67

See merge request !19
parents 063c377b 6f44aea3
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with 139 additions and 116 deletions
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
+ 6
− 2
View file @ 3a0b6423
...@@ -28,7 +28,11 @@ object BiopetExecutable { ...@@ -28,7 +28,11 @@ object BiopetExecutable {
nl.lumc.sasc.biopet.tools.FindRepeatsPacBio, nl.lumc.sasc.biopet.tools.FindRepeatsPacBio,
nl.lumc.sasc.biopet.tools.BedToInterval, nl.lumc.sasc.biopet.tools.BedToInterval,
nl.lumc.sasc.biopet.tools.MpileupToVcf, nl.lumc.sasc.biopet.tools.MpileupToVcf,
nl.lumc.sasc.biopet.tools.FastqSplitter) nl.lumc.sasc.biopet.tools.FastqSplitter,
nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
nl.lumc.sasc.biopet.tools.SageCountFastq,
nl.lumc.sasc.biopet.tools.SageCreateLibrary,
nl.lumc.sasc.biopet.tools.SageCreateTagCounts)
) )
/** /**
...@@ -37,7 +41,7 @@ object BiopetExecutable { ...@@ -37,7 +41,7 @@ object BiopetExecutable {
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
def toBulletedList(m: List[MainCommand], kind: String = "", bullet: String = "-") = def toBulletedList(m: List[MainCommand], kind: String = "", bullet: String = "-") =
"Available %ss:\n ".format(kind) + bullet + " " + m.map(x => x.commandName).sorted.mkString("\n " + bullet + " ") "Available %s(s):\n ".format(kind) + bullet + " " + m.map(x => x.commandName).sorted.mkString("\n " + bullet + " ")
def usage(module: String = null): String = { def usage(module: String = null): String = {
if (module != null) checkModule(module) if (module != null) checkModule(module)
......
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+ 7
− 3
View file @ 3a0b6423
...@@ -8,7 +8,11 @@ import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles ...@@ -8,7 +8,11 @@ import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import nl.lumc.sasc.biopet.scripts.PrefixFastq import nl.lumc.sasc.biopet.scripts.PrefixFastq
import nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts
import nl.lumc.sasc.biopet.scripts.SquishBed import nl.lumc.sasc.biopet.scripts.SquishBed
import nl.lumc.sasc.biopet.tools.SageCountFastq
import nl.lumc.sasc.biopet.tools.SageCreateLibrary
import nl.lumc.sasc.biopet.tools.SageCreateTagCounts
import org.broadinstitute.gatk.queue.QScript import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.function._ import org.broadinstitute.gatk.queue.function._
...@@ -64,7 +68,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript { ...@@ -64,7 +68,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
} }
if (tagsLibrary == null) { if (tagsLibrary == null) {
val cdl = new CreateDeepsageLibrary(this) val cdl = new SageCreateLibrary(this)
cdl.input = transcriptome cdl.input = transcriptome
cdl.output = outputDir + "taglib/tag.lib" cdl.output = outputDir + "taglib/tag.lib"
cdl.noAntiTagsOutput = outputDir + "taglib/no_antisense_genes.txt" cdl.noAntiTagsOutput = outputDir + "taglib/no_antisense_genes.txt"
...@@ -181,12 +185,12 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript { ...@@ -181,12 +185,12 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
} }
def addTablibCounts(fastq:File, outputPrefix: String, outputDir: String) { def addTablibCounts(fastq:File, outputPrefix: String, outputDir: String) {
val countFastq = new CountFastq(this) val countFastq = new SageCountFastq(this)
countFastq.input = fastq countFastq.input = fastq
countFastq.output = outputDir + outputPrefix + ".raw.counts" countFastq.output = outputDir + outputPrefix + ".raw.counts"
add(countFastq) add(countFastq)
val createTagCounts = new CreateTagCounts(this) val createTagCounts = new SageCreateTagCounts(this)
createTagCounts.input = countFastq.output createTagCounts.input = countFastq.output
createTagCounts.tagLib = tagsLibrary createTagCounts.tagLib = tagsLibrary
createTagCounts.countSense = outputDir + outputPrefix + ".tagcount.sense.counts" createTagCounts.countSense = outputDir + outputPrefix + ".tagcount.sense.counts"
......
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
+ 8
− 6
View file @ 3a0b6423
...@@ -25,7 +25,7 @@ class BedToInterval(val root: Configurable) extends BiopetJavaCommandLineFunctio ...@@ -25,7 +25,7 @@ class BedToInterval(val root: Configurable) extends BiopetJavaCommandLineFunctio
override val defaultVmem = "8G" override val defaultVmem = "8G"
memoryLimit = Option(4.0) memoryLimit = Option(4.0)
override def commandLine = super.commandLine + required(input) + required(bamFile) + required(output) override def commandLine = super.commandLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
} }
object BedToInterval extends ToolCommand { object BedToInterval extends ToolCommand {
...@@ -45,13 +45,15 @@ object BedToInterval extends ToolCommand { ...@@ -45,13 +45,15 @@ object BedToInterval extends ToolCommand {
return bedToInterval return bedToInterval
} }
case class Args (inputFile:File = null, outputFile:File = null) extends AbstractArgs case class Args (inputFile:File = null, outputFile:File = null, bamFile:File = null) extends AbstractArgs
class OptParser extends AbstractOptParser { class OptParser extends AbstractOptParser {
opt[File]('I', "inputFile") required() valueName("<file>") action { (x, c) => opt[File]('I', "inputFile") required() valueName("<file>") action { (x, c) =>
c.copy(inputFile = x) } text("out is a required file property") c.copy(inputFile = x) }
opt[File]('o', "output") required() valueName("<file>") action { (x, c) => opt[File]('o', "output") required() valueName("<file>") action { (x, c) =>
c.copy(outputFile = x) } text("out is a required file property") c.copy(outputFile = x) }
opt[File]('b', "bam") required() valueName("<file>") action { (x, c) =>
c.copy(bamFile = x) }
} }
/** /**
...@@ -63,7 +65,7 @@ object BedToInterval extends ToolCommand { ...@@ -63,7 +65,7 @@ object BedToInterval extends ToolCommand {
val writer = new PrintWriter(commandArgs.outputFile) val writer = new PrintWriter(commandArgs.outputFile)
val inputSam = new SAMFileReader(commandArgs.inputFile) val inputSam = new SAMFileReader(commandArgs.bamFile)
val refs = for (SQ <- inputSam.getFileHeader.getSequenceDictionary.getSequences.toArray) yield { val refs = for (SQ <- inputSam.getFileHeader.getSequenceDictionary.getSequences.toArray) yield {
val record = SQ.asInstanceOf[SAMSequenceRecord] val record = SQ.asInstanceOf[SAMSequenceRecord]
writer.write("@SQ\tSN:" + record.getSequenceName + "\tLN:" + record.getSequenceLength + "\n") writer.write("@SQ\tSN:" + record.getSequenceName + "\tLN:" + record.getSequenceLength + "\n")
...@@ -72,7 +74,7 @@ object BedToInterval extends ToolCommand { ...@@ -72,7 +74,7 @@ object BedToInterval extends ToolCommand {
inputSam.close inputSam.close
val refsMap = Map(refs:_*) val refsMap = Map(refs:_*)
val bedFile = Source.fromFile(args(0)) val bedFile = Source.fromFile(commandArgs.inputFile)
for ( for (
line <- bedFile.getLines; line <- bedFile.getLines;
val split = line.split("\t") val split = line.split("\t")
......
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/BedtoolsCoverageToCounts.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
+ 17
− 15
View file @ 3a0b6423
package nl.lumc.sasc.biopet.pipelines.sage package nl.lumc.sasc.biopet.tools
import java.io.File import java.io.File
import java.io.PrintWriter import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output } import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._ import scala.collection.JavaConversions._
...@@ -27,26 +28,27 @@ class BedtoolsCoverageToCounts(val root: Configurable) extends BiopetJavaCommand ...@@ -27,26 +28,27 @@ class BedtoolsCoverageToCounts(val root: Configurable) extends BiopetJavaCommand
required("-o", output) required("-o", output)
} }
object BedtoolsCoverageToCounts { object BedtoolsCoverageToCounts extends ToolCommand {
var input: File = _ case class Args (input:File = null, output:File = null) extends AbstractArgs
var output: File = _
class OptParser extends AbstractOptParser {
opt[File]('I', "input") required() valueName("<file>") action { (x, c) =>
c.copy(input = x) }
opt[File]('o', "output") required() unbounded() valueName("<file>") action { (x, c) =>
c.copy(output = x) }
}
/** /**
* @param args the command line arguments * @param args the command line arguments
*/ */
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
for (t <- 0 until args.size) { val argsParser = new OptParser
args(t) match { val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
case "-I" => input = new File(args(t+1))
case "-o" => output = new File(args(t+1)) if (!commandArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + commandArgs.input)
case _ =>
}
}
if (input == null || !input.exists) throw new IllegalStateException("Input file not found, use -I")
if (output == null) throw new IllegalStateException("Output file not found, use -o")
val counts:Map[String, Long] = Map() val counts:Map[String, Long] = Map()
for (line <- Source.fromFile(input).getLines) { for (line <- Source.fromFile(commandArgs.input).getLines) {
val values = line.split("\t") val values = line.split("\t")
val gene = values(3) val gene = values(3)
val count = values(6).toLong val count = values(6).toLong
...@@ -56,7 +58,7 @@ object BedtoolsCoverageToCounts { ...@@ -56,7 +58,7 @@ object BedtoolsCoverageToCounts {
val sortedCounts:SortedMap[String, Long] = SortedMap(counts.toArray:_*) val sortedCounts:SortedMap[String, Long] = SortedMap(counts.toArray:_*)
val writer = new PrintWriter(output) val writer = new PrintWriter(commandArgs.output)
for ((seq,count) <- sortedCounts) { for ((seq,count) <- sortedCounts) {
if (count > 0) writer.println(seq + "\t" + count) if (count > 0) writer.println(seq + "\t" + count)
} }
......
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/CountFastq.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
+ 22
− 20
View file @ 3a0b6423
package nl.lumc.sasc.biopet.pipelines.sage package nl.lumc.sasc.biopet.tools
import java.io.File import java.io.File
import java.io.PrintWriter import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output } import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import org.biojava3.sequencing.io.fastq.{SangerFastqReader, StreamListener, Fastq} import org.biojava3.sequencing.io.fastq.{SangerFastqReader, StreamListener, Fastq}
...@@ -11,7 +12,7 @@ import scala.collection.SortedMap ...@@ -11,7 +12,7 @@ import scala.collection.SortedMap
import scala.collection.mutable.Map import scala.collection.mutable.Map
import java.io.FileReader import java.io.FileReader
class CountFastq(val root: Configurable) extends BiopetJavaCommandLineFunction { class SageCountFastq(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName javaMainClass = getClass.getName
@Input(doc = "Input fasta", shortName = "input", required = true) @Input(doc = "Input fasta", shortName = "input", required = true)
...@@ -28,29 +29,30 @@ class CountFastq(val root: Configurable) extends BiopetJavaCommandLineFunction { ...@@ -28,29 +29,30 @@ class CountFastq(val root: Configurable) extends BiopetJavaCommandLineFunction {
required("-o", output) required("-o", output)
} }
object CountFastq { object SageCountFastq extends ToolCommand {
var input: File = _ case class Args (input:File = null, output:File = null) extends AbstractArgs
var output: File = _
class OptParser extends AbstractOptParser {
opt[File]('I', "input") required() valueName("<file>") action { (x, c) =>
c.copy(input = x) }
opt[File]('o', "output") required() unbounded() valueName("<file>") action { (x, c) =>
c.copy(output = x) }
}
/** /**
* @param args the command line arguments * @param args the command line arguments
*/ */
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
for (t <- 0 until args.size) { val argsParser = new OptParser
args(t) match { val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
case "-I" => input = new File(args(t+1))
case "-o" => output = new File(args(t+1)) if (!commandArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + commandArgs.input)
case _ =>
}
}
if (input == null || !input.exists) throw new IllegalStateException("Input file not found, use -I")
if (output == null) throw new IllegalStateException("Output file not found, use -o")
val counts:Map[String, Long] = Map() val counts:Map[String, Long] = Map()
val reader = new SangerFastqReader val reader = new SangerFastqReader
var count = 0 var count = 0
System.err.println("Reading fastq file: " + input) logger.info("Reading fastq file: " + commandArgs.input)
val fileReader = new FileReader(input) val fileReader = new FileReader(commandArgs.input)
reader.stream(fileReader, new StreamListener { reader.stream(fileReader, new StreamListener {
def fastq(fastq:Fastq) { def fastq(fastq:Fastq) {
val seq = fastq.getSequence val seq = fastq.getSequence
...@@ -60,13 +62,13 @@ object CountFastq { ...@@ -60,13 +62,13 @@ object CountFastq {
if (count % 1000000 == 0) System.err.println(count + " sequences done") if (count % 1000000 == 0) System.err.println(count + " sequences done")
} }
}) })
System.err.println(count + " sequences done") logger.info(count + " sequences done")
System.err.println("Sorting") logger.info("Sorting")
val sortedCounts:SortedMap[String, Long] = SortedMap(counts.toArray:_*) val sortedCounts:SortedMap[String, Long] = SortedMap(counts.toArray:_*)
System.err.println("Writting outputfile: " + output) logger.info("Writting outputfile: " + commandArgs.output)
val writer = new PrintWriter(output) val writer = new PrintWriter(commandArgs.output)
for ((seq,count) <- sortedCounts) { for ((seq,count) <- sortedCounts) {
writer.println(seq + "\t" + count) writer.println(seq + "\t" + count)
} }
......
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/CreateDeepsageLibrary.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
+ 44
− 37
View file @ 3a0b6423
package nl.lumc.sasc.biopet.pipelines.sage package nl.lumc.sasc.biopet.tools
import java.io.File import java.io.File
import java.io.PrintWriter import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import org.biojava3.core.sequence.DNASequence import org.biojava3.core.sequence.DNASequence
import org.biojava3.core.sequence.io.FastaReaderHelper import org.biojava3.core.sequence.io.FastaReaderHelper
...@@ -10,8 +11,9 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output } ...@@ -10,8 +11,9 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.SortedMap import scala.collection.SortedMap
import scala.collection.mutable.{Map, Set} import scala.collection.mutable.{Map, Set}
import scala.collection.JavaConversions._ import scala.collection.JavaConversions._
import scala.util.matching.Regex
class CreateDeepsageLibrary(val root: Configurable) extends BiopetJavaCommandLineFunction { class SageCreateLibrary(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName javaMainClass = getClass.getName
@Input(doc = "Input fasta", shortName = "input", required = true) @Input(doc = "Input fasta", shortName = "input", required = true)
...@@ -37,22 +39,35 @@ class CreateDeepsageLibrary(val root: Configurable) extends BiopetJavaCommandLin ...@@ -37,22 +39,35 @@ class CreateDeepsageLibrary(val root: Configurable) extends BiopetJavaCommandLin
override def commandLine = super.commandLine + override def commandLine = super.commandLine +
required("-I", input) + required("-I", input) +
optional("-tag", tag) + optional("--tag", tag) +
optional("-length", length) + optional("--length", length) +
optional("-notag", noTagsOutput) + optional("--notag", noTagsOutput) +
optional("-noantitag", noAntiTagsOutput) + optional("--noantitag", noAntiTagsOutput) +
required("-o", output) required("-o", output)
} }
object CreateDeepsageLibrary { object SageCreateLibrary extends ToolCommand {
var tag = "CATG" case class Args (input:File = null, tag:String = "CATG", length:Int = 17,output:File = null, noTagsOutput:File = null,
var length = 17 noAntiTagsOutput:File = null, allGenesOutput:File = null) extends AbstractArgs
var input: File = _
var noTagsOutput: File = _ class OptParser extends AbstractOptParser {
var noAntiTagsOutput: File = _ opt[File]('I', "input") required() unbounded() valueName("<file>") action { (x, c) =>
var allGenesOutput: File = _ c.copy(input = x) }
var output: File = _ opt[File]('o', "output") required() unbounded() valueName("<file>") action { (x, c) =>
lazy val tagRegex = (tag + "[CATG]{" + length + "}").r c.copy(output = x) }
opt[String]("tag") required() unbounded() action { (x, c) =>
c.copy(tag = x) }
opt[Int]("length") required() unbounded() action { (x, c) =>
c.copy(length = x) }
opt[File]("noTagsOutput") required() unbounded() valueName("<file>") action { (x, c) =>
c.copy(noTagsOutput = x) }
opt[File]("noAntiTagsOutput") required() unbounded() valueName("<file>") action { (x, c) =>
c.copy(noAntiTagsOutput = x) }
opt[File]("allGenesOutput") required() unbounded() valueName("<file>") action { (x, c) =>
c.copy(allGenesOutput = x) }
}
var tagRegex: Regex = null
var geneRegex = """ENSG[0-9]{11}""".r var geneRegex = """ENSG[0-9]{11}""".r
val tagGenesMap: Map[String, TagGenes] = Map() val tagGenesMap: Map[String, TagGenes] = Map()
...@@ -73,24 +88,16 @@ object CreateDeepsageLibrary { ...@@ -73,24 +88,16 @@ object CreateDeepsageLibrary {
* @param args the command line arguments * @param args the command line arguments
*/ */
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
for (t <- 0 until args.size) { val argsParser = new OptParser
args(t) match { val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
case "-I" => input = new File(args(t+1))
case "-tag" => tag = args(t+1) if (!commandArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + commandArgs.input)
case "-length" => length = args(t+1).toInt
case "-o" => output = new File(args(t+1)) tagRegex = (commandArgs.tag + "[CATG]{" + commandArgs.length + "}").r
case "-notag" => noTagsOutput = new File(args(t+1))
case "-noantitag" => noAntiTagsOutput = new File(args(t+1))
case "-allgenes" => allGenesOutput = new File(args(t+1))
case _ =>
}
}
if (input == null || !input.exists) throw new IllegalStateException("Input file not found, use -I")
if (output == null) throw new IllegalStateException("Output file not found, use -o")
var count = 0 var count = 0
System.err.println("Reading fasta file") System.err.println("Reading fasta file")
val reader = FastaReaderHelper.readFastaDNASequence(input) val reader = FastaReaderHelper.readFastaDNASequence(commandArgs.input)
System.err.println("Finding tags") System.err.println("Finding tags")
for ((name, seq) <- reader) { for ((name, seq) <- reader) {
getTags(name, seq) getTags(name, seq)
...@@ -103,7 +110,7 @@ object CreateDeepsageLibrary { ...@@ -103,7 +110,7 @@ object CreateDeepsageLibrary {
val tagGenesMapSorted:SortedMap[String, TagGenes] = SortedMap(tagGenesMap.toArray:_*) val tagGenesMapSorted:SortedMap[String, TagGenes] = SortedMap(tagGenesMap.toArray:_*)
System.err.println("Writting output files") System.err.println("Writting output files")
val writer = new PrintWriter(output) val writer = new PrintWriter(commandArgs.output)
writer.println("#tag\tfirstTag\tAllTags\tFirstAntiTag\tAllAntiTags") writer.println("#tag\tfirstTag\tAllTags\tFirstAntiTag\tAllAntiTags")
for ((tag, genes) <- tagGenesMapSorted) { for ((tag, genes) <- tagGenesMapSorted) {
val line = tag + "\t" + genes.firstTag.mkString(",") + val line = tag + "\t" + genes.firstTag.mkString(",") +
...@@ -114,24 +121,24 @@ object CreateDeepsageLibrary { ...@@ -114,24 +121,24 @@ object CreateDeepsageLibrary {
} }
writer.close() writer.close()
if (noTagsOutput != null) { if (commandArgs.noTagsOutput != null) {
val writer = new PrintWriter(noTagsOutput) val writer = new PrintWriter(commandArgs.noTagsOutput)
for (gene <- allGenes if !tagGenes.contains(gene)) { for (gene <- allGenes if !tagGenes.contains(gene)) {
writer.println(gene) writer.println(gene)
} }
writer.close writer.close
} }
if (noAntiTagsOutput != null) { if (commandArgs.noAntiTagsOutput != null) {
val writer = new PrintWriter(noAntiTagsOutput) val writer = new PrintWriter(commandArgs.noAntiTagsOutput)
for (gene <- allGenes if !antiTagGenes.contains(gene)) { for (gene <- allGenes if !antiTagGenes.contains(gene)) {
writer.println(gene) writer.println(gene)
} }
writer.close writer.close
} }
if (allGenesOutput != null) { if (commandArgs.allGenesOutput != null) {
val writer = new PrintWriter(allGenesOutput) val writer = new PrintWriter(commandArgs.allGenesOutput)
for (gene <- allGenes) { for (gene <- allGenes) {
writer.println(gene) writer.println(gene)
} }
......
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/CreateTagCounts.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
+ 35
− 33
View file @ 3a0b6423
package nl.lumc.sasc.biopet.pipelines.sage package nl.lumc.sasc.biopet.tools
import java.io.File import java.io.File
import java.io.PrintWriter import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output } import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.io.Source import scala.io.Source
import scala.collection.mutable.Map import scala.collection.mutable.Map
import scala.collection.SortedMap import scala.collection.SortedMap
class CreateTagCounts(val root: Configurable) extends BiopetJavaCommandLineFunction { class SageCreateTagCounts(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName javaMainClass = getClass.getName
@Input(doc = "Raw count file", shortName = "input", required = true) @Input(doc = "Raw count file", shortName = "input", required = true)
...@@ -35,42 +36,43 @@ class CreateTagCounts(val root: Configurable) extends BiopetJavaCommandLineFunct ...@@ -35,42 +36,43 @@ class CreateTagCounts(val root: Configurable) extends BiopetJavaCommandLineFunct
override def commandLine = super.commandLine + override def commandLine = super.commandLine +
required("-I", input) + required("-I", input) +
required("-taglib", tagLib) + required("--taglib", tagLib) +
optional("-sense", countSense) + optional("--sense", countSense) +
optional("-allsense", countAllSense) + optional("--allsense", countAllSense) +
optional("-antisense", countAntiSense) + optional("--antisense", countAntiSense) +
optional("-allantisense", countAllAntiSense) optional("--allantisense", countAllAntiSense)
} }
object CreateTagCounts { object SageCreateTagCounts extends ToolCommand {
var input: File = _ case class Args (input:File = null, tagLib:File = null, countSense:File = null, countAllSense:File = null,
var tagLib: File = _ countAntiSense:File = null, countAllAntiSense:File = null) extends AbstractArgs
var countSense: File = _
var countAllSense: File = _ class OptParser extends AbstractOptParser {
var countAntiSense: File = _ opt[File]('I', "input") required() unbounded() valueName("<file>") action { (x, c) =>
var countAllAntiSense: File = _ c.copy(input = x) }
opt[File]('t', "tagLib") required() unbounded() valueName("<file>") action { (x, c) =>
c.copy(tagLib = x) }
opt[File]("countSense") unbounded() valueName("<file>") action { (x, c) =>
c.copy(countSense = x) }
opt[File]("countAllSense") unbounded() valueName("<file>") action { (x, c) =>
c.copy(countAllSense = x) }
opt[File]("countAntiSense") unbounded() valueName("<file>") action { (x, c) =>
c.copy(countAntiSense = x) }
opt[File]("countAllAntiSense") unbounded() valueName("<file>") action { (x, c) =>
c.copy(countAllAntiSense = x) }
}
/** /**
* @param args the command line arguments * @param args the command line arguments
*/ */
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
val argsParser = new OptParser
val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
for (t <- 0 until args.size) { if (!commandArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + commandArgs.input)
args(t) match {
case "-I" => input = new File(args(t+1))
case "-taglib" => tagLib = new File(args(t+1))
case "-sense" => countSense = new File(args(t+1))
case "-allsense" => countAllSense = new File(args(t+1))
case "-antisense" => countAntiSense = new File(args(t+1))
case "-allantisense" => countAllAntiSense = new File(args(t+1))
case _ =>
}
}
if (input == null || !input.exists) throw new IllegalStateException("Input file not found, use -I")
if (tagLib == null) throw new IllegalStateException("Output file not found, use -o")
val rawCounts: Map[String, Long] = Map() val rawCounts: Map[String, Long] = Map()
for (line <- Source.fromFile(input).getLines) { for (line <- Source.fromFile(commandArgs.input).getLines) {
val values = line.split("\t") val values = line.split("\t")
val gene = values(0) val gene = values(0)
val count = values(1).toLong val count = values(1).toLong
...@@ -83,7 +85,7 @@ object CreateTagCounts { ...@@ -83,7 +85,7 @@ object CreateTagCounts {
val antiSenseCounts: Map[String, Long] = Map() val antiSenseCounts: Map[String, Long] = Map()
val allAntiSenseCounts: Map[String, Long] = Map() val allAntiSenseCounts: Map[String, Long] = Map()
for (line <- Source.fromFile(tagLib).getLines if !line.startsWith("#")) { for (line <- Source.fromFile(commandArgs.tagLib).getLines if !line.startsWith("#")) {
val values = line.split("\t") val values = line.split("\t")
val tag = values(0) val tag = values(0)
val sense = values(1) val sense = values(1)
...@@ -126,9 +128,9 @@ object CreateTagCounts { ...@@ -126,9 +128,9 @@ object CreateTagCounts {
writer.close writer.close
} }
} }
writeFile(countSense, senseCounts) writeFile(commandArgs.countSense, senseCounts)
writeFile(countAllSense, allSenseCounts) writeFile(commandArgs.countAllSense, allSenseCounts)
writeFile(countAntiSense, antiSenseCounts) writeFile(commandArgs.countAntiSense, antiSenseCounts)
writeFile(countAllAntiSense, allAntiSenseCounts) writeFile(commandArgs.countAllAntiSense, allAntiSenseCounts)
} }
} }
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