cli: implements variant plink cli, #126

hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/AnalysisExecutor.java

@@ -6,6 +6,9 @@
  * Created by jtarraga on 30/01/17.
  */
 public abstract class AnalysisExecutor {
+
+    public static String metadataExtension = ".meta.json";
+
     protected String datasetName;
     protected SparkSession sparkSession;
 

hpg-bigdata-analysis/src/main/java/org/opencb/hpg/bigdata/analysis/variant/adaptors/PlinkAdaptor.java

@@ -0,0 +1,80 @@
+package org.opencb.hpg.bigdata.analysis.variant.adaptors;
+
+import org.opencb.hpg.bigdata.analysis.AnalysisExecutor;
+import org.opencb.hpg.bigdata.analysis.AnalysisExecutorException;
+
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Created by jtarraga on 09/06/17.
+ */
+public class PlinkAdaptor extends AnalysisExecutor {
+    private String inFilename;
+    private String metaFilename;
+    private String outDirname;
+
+    private int splitSize;
+    private List<String> plinkParams;
+    private Map<String, String> filterOptions;
+
+    public PlinkAdaptor(String inFilename, String metaFilename, String outDirname) {
+        this.inFilename = inFilename;
+        this.metaFilename = inFilename + AnalysisExecutor.metadataExtension;
+        this.outDirname = outDirname;
+    }
+
+    @Override
+    public void execute() throws AnalysisExecutorException {
+        System.out.println("plink params = " + plinkParams);
+        System.out.println("filter options = " + filterOptions);
+    }
+
+    public String getInFilename() {
+        return inFilename;
+    }
+
+    public void setInFilename(String inFilename) {
+        this.inFilename = inFilename;
+    }
+
+    public String getMetaFilename() {
+        return metaFilename;
+    }
+
+    public void setMetaFilename(String metaFilename) {
+        this.metaFilename = metaFilename;
+    }
+
+    public String getOutDirname() {
+        return outDirname;
+    }
+
+    public void setOutDirname(String outDirname) {
+        this.outDirname = outDirname;
+    }
+
+    public int getSplitSize() {
+        return splitSize;
+    }
+
+    public void setSplitSize(int splitSize) {
+        this.splitSize = splitSize;
+    }
+
+    public List<String> getPlinkParams() {
+        return plinkParams;
+    }
+
+    public void setPlinkParams(List<String> plinkParams) {
+        this.plinkParams = plinkParams;
+    }
+
+    public Map<String, String> getFilterOptions() {
+        return filterOptions;
+    }
+
+    public void setFilterOptions(Map<String, String> filterOptions) {
+        this.filterOptions = filterOptions;
+    }
+}

hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/CliUtils.java

@@ -13,9 +13,7 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
+import java.util.*;
 
 import static java.nio.file.Paths.get;
 
@@ -212,4 +210,25 @@ public static VariantCommandOptions createVariantCommandOptions(
 
         return parser.getVariantCommandOptions();
     }
+
+    public static Map<String, String> getFilterMap(VariantCommandOptions.PlinkVariantCommandOptions options) {
+        Map<String, String> mapFilter = new HashMap<>();
+
+        // regions
+        if (StringUtils.isNotEmpty(options.regions)) {
+            mapFilter.put("regions", options.regions);
+        }
+
+        // types
+        if (StringUtils.isNotEmpty(options.types)) {
+            mapFilter.put("types", options.types);
+        }
+
+        // biotypes
+        if (StringUtils.isNotEmpty(options.biotypes)) {
+            mapFilter.put("biotypes", options.biotypes);
+        }
+
+        return mapFilter;
+    }
 }

hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/LocalCliOptionsParser.java

@@ -85,6 +85,7 @@ public LocalCliOptionsParser() {
         variantSubCommands.addCommand("view", variantCommandOptions.viewVariantCommandOptions);
         variantSubCommands.addCommand("query", variantCommandOptions.queryVariantCommandOptions);
         variantSubCommands.addCommand("metadata", variantCommandOptions.metadataVariantCommandOptions);
+        variantSubCommands.addCommand("plink", variantCommandOptions.plinkVariantCommandOptions);
         variantSubCommands.addCommand("rvtests", variantCommandOptions.rvtestsVariantCommandOptions);
         variantSubCommands.addCommand("association", variantCommandOptions.associationVariantCommandOptions);
 

hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/executors/VariantCommandExecutor.java

@@ -45,6 +45,7 @@
 import org.opencb.hpg.bigdata.analysis.variant.LinearRegressionAnalysis;
 import org.opencb.hpg.bigdata.analysis.variant.LogisticRegressionAnalysis;
 import org.opencb.hpg.bigdata.analysis.variant.RvTestsAdaptor;
+import org.opencb.hpg.bigdata.analysis.variant.adaptors.PlinkAdaptor;
 import org.opencb.hpg.bigdata.app.cli.CommandExecutor;
 import org.opencb.hpg.bigdata.app.cli.local.CliUtils;
 import org.opencb.hpg.bigdata.app.cli.local.options.VariantCommandOptions;
@@ -103,6 +104,9 @@ public void execute() throws Exception {
             case "metadata":
                 metadata();
                 break;
+            case "plink":
+                plink();
+                break;
             case "rvtests":
                 rvtests();
                 break;
@@ -863,6 +867,21 @@ public void rvtests() throws Exception {
         rvtests.run00(variantCommandOptions.rvtestsVariantCommandOptions.datasetId);
     }
 
+    public void plink() throws Exception {
+        PlinkAdaptor plink = new PlinkAdaptor(variantCommandOptions.plinkVariantCommandOptions.inFilename,
+                variantCommandOptions.plinkVariantCommandOptions.metaFilename,
+                variantCommandOptions.plinkVariantCommandOptions.outDirname);
+
+        plink.setPlinkParams(variantCommandOptions.plinkVariantCommandOptions.plinkParams);
+        plink.setSplitSize(variantCommandOptions.plinkVariantCommandOptions.splitSize);
+        plink.setFilterOptions(CliUtils.getFilterMap(variantCommandOptions.plinkVariantCommandOptions));
+
+        plink.execute();
+
+////        rvtests.run(variantCommandOptions.rvtestsVariantCommandOptions.datasetId);
+        //rvtests.run00(variantCommandOptions.rvtestsVariantCommandOptions.datasetId);
+    }
+
     public void assoc() throws Exception {
         // check input file
         File metaFile = new File(variantCommandOptions.associationVariantCommandOptions.input + ".meta.json");

hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/options/VariantCommandOptions.java

@@ -7,6 +7,8 @@
 import org.apache.parquet.hadoop.ParquetWriter;
 import org.opencb.hpg.bigdata.app.cli.local.LocalCliOptionsParser;
 
+import java.util.List;
+
 /**
  * Created by jtarraga on 01/06/17.
  */
@@ -20,6 +22,7 @@ public class VariantCommandOptions {
     public ViewVariantCommandOptions viewVariantCommandOptions;
     public QueryVariantCommandOptions queryVariantCommandOptions;
     public MetadataVariantCommandOptions metadataVariantCommandOptions;
+    public PlinkVariantCommandOptions plinkVariantCommandOptions;
     public RvTestsVariantCommandOptions rvtestsVariantCommandOptions;
     public AssociationVariantCommandOptions associationVariantCommandOptions;
 
@@ -36,6 +39,7 @@ public VariantCommandOptions(LocalCliOptionsParser.CommonCommandOptions commonCo
         this.viewVariantCommandOptions = new ViewVariantCommandOptions();
         this.queryVariantCommandOptions = new QueryVariantCommandOptions();
         this.metadataVariantCommandOptions = new MetadataVariantCommandOptions();
+        this.plinkVariantCommandOptions = new PlinkVariantCommandOptions();
         this.rvtestsVariantCommandOptions = new RvTestsVariantCommandOptions();
         this.associationVariantCommandOptions = new AssociationVariantCommandOptions();
     }
@@ -354,6 +358,117 @@ public class RvTestsVariantCommandOptions {
         public String confFilename;
     }
 
+    @Parameters(commandNames = {"plink"}, commandDescription = "Execute the 'plink' program")
+    public class PlinkVariantCommandOptions {
+
+        @ParametersDelegate
+        public LocalCliOptionsParser.CommonCommandOptions commonOptions = commonCommandOptions;
+
+
+        @Parameter(names = {"-i", "--input"}, description = "Input file name (in Avro/Parquet file format)",
+                required = true, arity = 1)
+        public String inFilename;
+
+        @Parameter(names = {"-m", "--metadata"}, description = "Input metadata file name", required = true, arity = 1)
+        public String metaFilename;
+
+        @Parameter(names = {"--dataset"}, description = "Target dataset", arity = 1)
+        public String datasetId = null;
+
+        @Parameter(names = {"--plink-params"}, description = "List of space-separated key=value parameters necessary to"
+                + " run the plink program", required = true, variableArity = true)
+        public List<String> plinkParams;
+
+        @Parameter(names = {"--split-size"}, description = "Split size. Range 10000000-100000000", arity = 1)
+        public int splitSize = 10000000;
+
+        @Parameter(names = {"-o", "--output"}, description = "Output directory name to save the plink results",
+                required = true, arity = 1)
+        public String outDirname;
+
+        // filter parameters
+        @Parameter(names = {"--id"}, description = "Filter ID; comma separated list of IDs, e.g.:"
+                + " \"rs312411,rs421225\"", arity = 1)
+        public String ids;
+
+        @Parameter(names = {"--id-file"}, description = "Filter ID that are stored in a file, one ID per line,"
+                + " e.g.: rs312411", arity = 1)
+        public String idFilename;
+
+        @Parameter(names = {"--type"}, description = "Filter type; comma separated list of IDs, e.g.:"
+                + " \"INDEL,SNP,SNV\"", arity = 1)
+        public String types;
+
+        @Parameter(names = {"--s", "--study"}, description = "Filter study; comma separated list of study names",
+                arity = 1)
+        public String studies;
+
+        @Parameter(names = {"--biotype"}, description = "Filter biotype; comma separated list of biotype names,"
+                + " e.g.: protein_coding, pseudogene", arity = 1)
+        public String biotypes;
+
+        @Parameter(names = {"-r", "--region"}, description = "Filter region; comma separated list of regions,"
+                + " e.g.: 1:300000-400000000,15:343453463-8787665654", arity = 1)
+        public String regions;
+
+        @Parameter(names = {"--region-file"}, description = "Filter regions that are stored in a file, one region"
+                + " per line,  e.g.: 1:6700000-560000000", arity = 1)
+        public String regionFilename;
+
+        @Parameter(names = {"--maf"}, description = "QuerFilter Minor Allele Frequency of a given study and"
+                + " cohort. Use the following format enclosed with double quotes: \"study_name::cohort_name"
+                + "[<|>|<=|>=|==|!=]value\", e.g.: \"1000g::all>0.4\"", arity = 1)
+        public String maf;
+
+        @Parameter(names = {"--mgf"}, description = "Filter Minor Genotype Frequency of a given study and"
+                + " cohort. Use the following format enclosed with double quotes: \"study_name::cohort_name"
+                + "[<|>|<=|>=|==|!=]value\", e.g.: \"1000g::all>0.18198\"", arity = 1)
+        public String mgf;
+
+        @Parameter(names = {"--ct", "--consequence-type"}, description = "Filter Sequence Ontology term names or"
+                + " accession codes; comma separated (use double quotes if you provide term names), e.g.:"
+                + " \"transgenic insertion,SO:32234,SO:00124\"", arity = 1)
+        public String consequenceTypes;
+
+        @Parameter(names = {"--gene"}, description = "Filter gene; comma separated list of gene names, e.g.:"
+                + " \"BIN3,ZNF517\"", arity = 1)
+        public String genes;
+
+        @Parameter(names = {"--clinvar"}, description = "Filter clinvar (accession); comma separated list of"
+                + " accessions", arity = 1)
+        public String clinvar;
+
+        @Parameter(names = {"--cosmic"}, description = "Filter cosmic (mutation ID); comma separated list of"
+                + " mutations IDs", arity = 1)
+        public String cosmic;
+
+        @Parameter(names = {"--conservation"}, description = "Filter conservation scores (phastCons, phylop, gerp);"
+                + "comma separated list of scores and enclosed with double quotes, e.g.: \"phylop<0.3,phastCons<0.1\"",
+                arity = 1)
+        public String conservScores;
+
+        @Parameter(names = {"--ps", "--protein-substitution"}, description = "Filter protein substitution scores"
+                + " (polyphen, sift); comma separated list of scores and enclosed with double quotes, e.g.:"
+                + "\"polyphen>0.3,sift>0.6\"", arity = 1)
+        public String substScores;
+
+        @Parameter(names = {"--pf", "--population-frequency"}, description = "Filter alternate population"
+                + " frequency of a given study: \"study_name::population_name[<|>|<=|>=|==|!=]frequency_value\", e.g.: "
+                + " \"1000g::CEU<0.4\"",
+                arity = 1)
+        public String pf;
+
+        @Parameter(names = {"--pmaf", "--population-maf"}, description = "Filter population minor allele frequency"
+                + " of a given study: \"study_name:: population_name[<|>|<=|>=|==|!=]frequency_value\", e.g.: "
+                + "\"1000g::PJL<=0.25\"", arity = 1)
+        public String pmaf;
+
+        @Parameter(names = {"--sample"}, description = "Filter sample names; comma separated list of sample names",
+                arity = 1)
+        public String samples;
+        // end of filter parameters
+    }
+
     @Parameters(commandNames = {"association"}, commandDescription = "Execute association tests such as chi-square,"
             + " linear and logistic regressions for additive, dominant or recessive genetic models")
     public class AssociationVariantCommandOptions {