net.maizegenetics.analysis.gbs.pana.PanAUsageExample Maven / Gradle / Ivy
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package net.maizegenetics.analysis.gbs.pana;
import java.io.File;
import java.util.Arrays;
import net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin;
/**
*
* @author Fei Lu
*/
public class PanAUsageExample {
public PanAUsageExample () {
this.h5ToAnchorPlugin();
//this.splitTBTPlugin();
//this.buildTagBlockPositionPlugin();
//this.splitTagBlockPositionPlugin();
//this.GWASMappingPlugin();
//this.mergeMappingResultPlugin();
//this.mappingResultToTagGWASMapPlugin();
//this.tagMapToFastaPlugin();
//this.alignmentWithBowtie2();
//this.samToMultiPositionTOPMPlugin();
//this.addPosToTagMapPlugin();
//this.buildTrainingSetPlugin();
//this.modelTrainingPlugin();
//this.predictionPlugin();
//this.filterTagMapPlugin();
this.readDigestPlugin();
//this.mergeMultipleTagCountPlugin();
//this.buildPivotTBTPlugin();
}
public void readDigestPlugin () {
String rawSeqDirS = "M:\\pipelineTest\\PanA\\Illumina\\fastq\\";
String keyFileS = "M:\\pipelineTest\\PanA\\key\\keyFastq.txt";
String recSeq = "GCTG";
int customTagLength = 96;
String outputDirS = "M:\\pipelineTest\\PanA\\tagCount\\";
String arguments = "-i " + rawSeqDirS + " -k " + keyFileS + " -s " + recSeq + " -l " + String.valueOf(customTagLength)+ " -f 0 -o " + outputDirS;
String[] args = arguments.split(" ");
PanAReadDigestPlugin rdp = new PanAReadDigestPlugin();
rdp.setParameters(args);
rdp.performFunction(null);
}
public void mergeMultipleTagCountPlugin () {
String tagCountDirectory = "M:\\pipelineTest\\PanA\\tagCount\\";
String masterTagCount = "M:\\pipelineTest\\PanA\\masterTagCount\\master.cnt";
int minCount = 1;
String arguments = "-i " + tagCountDirectory + " -o " + masterTagCount + " -c " + String.valueOf(minCount);
String[] args = arguments.split(" ");
MergeMultipleTagCountPlugin p = new MergeMultipleTagCountPlugin();
p.setParameters(args);
p.performFunction(null);
}
public void buildPivotTBTPlugin () {
String masterTagCountFileS = "M:\\pipelineTest\\PanA\\masterTagCount\\master.cnt";
String tagCountDirS = "M:\\pipelineTest\\PanA\\tagCount";
String tbtFileS = "M:\\pipelineTest\\PanA\\tbt\\TBT_shotgun_pivot.h5";
String arguments = "-m " + masterTagCountFileS + " -d " + tagCountDirS + " -o " + tbtFileS;
String[] args = arguments.split(" ");
PanABuildPivotTBTPlugin p = new PanABuildPivotTBTPlugin();
p.setParameters(args);
p.performFunction(null);
}
public void h5ToAnchorPlugin () {
String h5GentoypeFileS = "M:\\pipelineTest\\PanA\\genotype\\GBS27.1024sites.T5.imp.hmp.h5";
String sBitGenotypeFileS = "M:\\pipelineTest\\PanA\\genotype\\GBS27.1024sites.sBit.h5";
String arguments = "-i " + h5GentoypeFileS + " -o " + sBitGenotypeFileS;
String[] args = arguments.split(" ");
PanAH5ToAnchorPlugin hta = new PanAH5ToAnchorPlugin();
hta.setParameters(args);
hta.performFunction(null);
}
public void splitTBTPlugin () {
String inputTBTS = "M:\\pipelineTest\\PanA\\tbt\\TBTHDF5_4096_tags_mergedtaxa_pivot_20120921.h5";
String outputDirS = "M:\\pipelineTest\\PanA\\tbt\\subTBT\\";
String chunkSize = "1000";
String arguments = "-i " + inputTBTS + " -s " + chunkSize + " -o " + outputDirS;
String[] args = arguments.split(" ");
PanASplitTBTPlugin sbp = new PanASplitTBTPlugin();
sbp.setParameters(args);
sbp.performFunction(null);
}
public void buildTagBlockPositionPlugin () {
String tbtHDF5 = "M:\\pipelineTest\\PanA\\tbt\\TBTHDF5_4096_tags_mergedtaxa_pivot_20120921.h5";
String topmFileS = "M:\\production\\geneticMapping\\tagBlock\\AllZeaGBSv2.6ProdTOPM_20130605.topm.h5";
String blockFileS = "M:\\pipelineTest\\PanA\\tbp\\tagBlock.tbp";
int TOPMVersionValue = 1;
String arguments = "-t " + tbtHDF5 + " -p " + topmFileS + " -v " + String.valueOf(TOPMVersionValue) + " -o " + blockFileS;
String[] args = arguments.split(" ");
PanABuildTagBlockPosPlugin tbp = new PanABuildTagBlockPosPlugin();
tbp.setParameters(args);
tbp.performFunction(null);
}
public void splitTagBlockPositionPlugin () {
String blockFileS = "M:\\pipelineTest\\PanA\\tbp\\tagBlock.tbp";
String outputDirS = "M:\\pipelineTest\\PanA\\tbp\\subTBP";
String chunkSize = "1000";
String arguments = "-i " + blockFileS + " -s " + chunkSize + " -o " + outputDirS;
String[] args = arguments.split(" ");
PanASplitTagBlockPosPlugin stb = new PanASplitTagBlockPosPlugin();
stb.setParameters(args);
stb.performFunction(null);
}
public void GWASMappingPlugin () {
String sBitGenotypeFileS = "M:\\pipelineTest\\PanA\\genotype\\GBS27.1024sites.sBit.h5";
String outDirS = "M:\\pipelineTest\\PanA\\gwasResult\\sub\\";
String tbtDirS = "M:\\pipelineTest\\PanA\\tbt\\subTBT\\";
String tbpDirS = "M:\\pipelineTest\\PanA\\tbp\\subTBP\\";
File[] tbts = new File (tbtDirS).listFiles();
File[] tbps = new File (tbpDirS).listFiles();
Arrays.sort(tbts);
Arrays.sort(tbps);
for (int i = 0; i < tbts.length; i++) {
String arguments = "-g " + sBitGenotypeFileS + " -t " + tbts[i].getAbsolutePath() + " -b " + tbps[i].getAbsolutePath() + " -o " + outDirS + " -c max -s 1000 -cs 0 -ce 1";
String[] args = arguments.split(" ");
PanATagGWASMappingPlugin tgm = new PanATagGWASMappingPlugin();
tgm.setParameters(args);
tgm.performFunction(null);
}
}
public void mergeMappingResultPlugin () {
String subResultDirS = "M:\\pipelineTest\\PanA\\gwasResult\\sub\\";
String mergedResultFileS = "M:\\pipelineTest\\PanA\\gwasResult\\pivotTBT.gwas.txt";
String arguments = "-i " + subResultDirS + " -o " + mergedResultFileS;
String[] args = arguments.split(" ");
PanAMergeMappingResultPlugin mmr = new PanAMergeMappingResultPlugin();
mmr.setParameters(args);
mmr.performFunction(null);
}
public void mappingResultToTagGWASMapPlugin () {
String mappingResultFileS = "M:\\pipelineTest\\PanA\\gwasResult\\pivotTBT.gwas.txt";
String tagCountFileS = "M:/production/v3gbs/tagCount/AllZeaMasterTags_c10_20120606.cnt";
String tagGWASMapFileS = "M:\\pipelineTest\\PanA\\tagMap\\tagGWASMap.h5";
String arguments = "-i " + mappingResultFileS + " -t " + tagCountFileS + " -o " + tagGWASMapFileS;
String[] args = arguments.split(" ");
PanABuildTagGWASMapPlugin mrtg = new PanABuildTagGWASMapPlugin();
mrtg.setParameters(args);
mrtg.performFunction(null);
}
public void tagMapToFastaPlugin () {
String tagGWASMapFileS = "M:\\pipelineTest\\PanA\\tagMap\\tagGWASMap.h5";
String fastaFileS = "M:\\pipelineTest\\PanA\\alignment\\tagGWASMap.fa";
String arguments = "-i " + tagGWASMapFileS + " -o " + fastaFileS;
String[] args = arguments.split(" ");
PanATagMapToFastaPlugin tmtf = new PanATagMapToFastaPlugin();
tmtf.setParameters(args);
tmtf.performFunction(null);
}
public void alignmentWithBowtie2 () {
String command = "bowtie2 -x ZmB73_RefGen_v2.fa -f tagGWASMap.fa -k 2 --very-sensitive-local -p 8 -S tagGWASMap.sam";
}
public void samToMultiPositionTOPMPlugin () {
String samFileS = "M:\\pipelineTest\\PanA\\alignment\\tagGWASMap.sam";
String tagGWASMapFileS = "M:\\pipelineTest\\PanA\\tagMap\\tagGWASMap.h5";
String topmV3FileS = "M:\\pipelineTest\\PanA\\alignment\\tagGWASMap.v3.topm.h5";
String arguments = "-i " + samFileS + " -t " + tagGWASMapFileS + " -o " + topmV3FileS;
String[] args = arguments.split(" ");
PanASamToMultiPositionTOPMPlugin stt = new PanASamToMultiPositionTOPMPlugin();
stt.setParameters(args);
stt.performFunction(null);
}
public void addPosToTagMapPlugin () {
String tagGWASMapFileS = "M:\\pipelineTest\\PanA\\tagMap\\tagGWASMap.h5";
String topmV3FileS = "M:\\pipelineTest\\PanA\\alignment\\tagGWASMap.v3.topm.h5";
String arguments = "-i " + tagGWASMapFileS + " -t " + topmV3FileS;
String[] args = arguments.split(" ");
PanAAddPosToTagMapPlugin p = new PanAAddPosToTagMapPlugin();
p.setParameters(args);
p.performFunction(null);
}
public void buildTrainingSetPlugin () {
String tagGWASMapFileS = "M:\\pipelineTest\\PanA\\tagMap\\tagGWASMap.h5";
String trainingSetFileS = "M:\\pipelineTest\\PanA\\training\\uniqueRefTrain.arff";
String rScriptPath = "C:\\Users\\fl262\\Documents\\R\\R-3.0.2\\bin\\Rscript.exe";
String boxcoxParemeterFileS = "M:\\pipelineTest\\PanA\\training\\boxcoxParemeter.txt";
String arguments = "-m " + tagGWASMapFileS + " -t " + trainingSetFileS + " -r " + rScriptPath + " -b " + boxcoxParemeterFileS;
String[] args = arguments.split(" ");
PanABuildTrainingSetPlugin p = new PanABuildTrainingSetPlugin();
p.setParameters(args);
p.performFunction(null);
}
public void modelTrainingPlugin () {
String trainingSetFileS = "M:\\pipelineTest\\PanA\\training\\uniqueRefTrain.arff";
String wekaPath = "E:\\Database\\Weka-3-6\\weka.jar";
String modelFileS = "M:\\pipelineTest\\PanA\\training\\m5.mod";
String trainingReportDirS = "M:\\pipelineTest\\PanA\\training\\report\\";
String arguments = "-t " + trainingSetFileS + " -w " + wekaPath + " -m " + modelFileS + " -r " + trainingReportDirS;
String[] args = arguments.split(" ");
PanAModelTrainingPlugin p = new PanAModelTrainingPlugin();
p.setParameters(args);
p.performFunction(null);
}
public void predictionPlugin () {
String wekaPath = "E:\\Database\\Weka-3-6\\weka.jar";
String tagGWASMapFileS = "M:\\pipelineTest\\PanA\\tagMap\\tagGWASMap.h5";
String modelFileS = "M:\\pipelineTest\\PanA\\training\\m5.mod";
String boxcoxParemeterFileS = "M:\\pipelineTest\\PanA\\training\\boxcoxParemeter.txt";
String arguments = "-t " + tagGWASMapFileS + " -w " + wekaPath + " -m " + modelFileS + " -b " + boxcoxParemeterFileS;
String[] args = arguments.split(" ");
PanAPredictionPlugin p = new PanAPredictionPlugin();
p.setParameters(args);
p.performFunction(null);
}
public void filterTagMapPlugin () {
String tagGWASMapFileS = "M:\\pipelineTest\\PanA\\tagMap\\tagGWASMap.h5";
int distanceCutoff = Integer.MAX_VALUE;
String anchorFileS = "M:\\pipelineTest\\PanA\\togm\\anchor.txt" ;
String arguments = "-t " + tagGWASMapFileS + " -a " + anchorFileS + " -c " + String.valueOf(distanceCutoff);
String[] args = arguments.split(" ");
PanAFilteringTagMapPlugin p = new PanAFilteringTagMapPlugin();
p.setParameters(args);
p.performFunction(null);
}
public static void main (String[] args) {
new PanAUsageExample();
}
}