analysis: major improvements in rvtests and plink analsys #125 #128

hpg-bigdata-analysis/pom.xml

@@ -84,6 +84,11 @@
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
         </dependency>
+        <dependency>
+            <groupId>com.beust</groupId>
+            <artifactId>jcommander</artifactId>
+            <version>1.58</version>
+        </dependency>
     </dependencies>
 
 </project>

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

@@ -4,15 +4,19 @@
  * Created by jtarraga on 30/01/17.
  */
 public abstract class AnalysisExecutor {
-    protected String datasetName;
+    protected String studyId;
 
-    public String getDatasetName() {
-        return datasetName;
+    protected AnalysisExecutor(String studyId) {
+        this.studyId = studyId;
     }
 
-    public void setDatasetName(String datasetName) {
-        this.datasetName = datasetName;
+    protected String studyId() {
+        return studyId;
     }
 
-    public abstract void execute() throws AnalysisExecutorException;
+    protected void setStudyId(String studyId) {
+        this.studyId = studyId;
+    }
+
+    protected abstract void execute() throws AnalysisExecutorException;
 }

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

@@ -0,0 +1,105 @@
+package org.opencb.hpg.bigdata.analysis.variant;
+
+import com.beust.jcommander.Parameter;
+
+public class FilterParameters {
+    @Parameter(names = {"--id"}, description = "Query for ID; comma separated list of IDs, e.g.:"
+            + " \"rs312411,rs421225\"", arity = 1)
+    public String ids;
+
+    @Parameter(names = {"--id-file"}, description = "Query for ID that are stored in a file, one ID per line,"
+            + " e.g.: rs312411", arity = 1)
+    public String idFilename;
+
+    @Parameter(names = {"--type"}, description = "Query for type; comma separated list of IDs, e.g.:"
+            + " \"INDEL,SNP,SNV\"", arity = 1)
+    public String types;
+
+    @Parameter(names = {"--s", "--study"}, description = "Query for study; comma separated list of study names",
+            arity = 1)
+    public String studies;
+
+    @Parameter(names = {"--biotype"}, description = "Query for biotype; comma separated list of biotype names,"
+            + " e.g.: protein_coding, pseudogene", arity = 1)
+    public String biotypes;
+
+    @Parameter(names = {"-r", "--region"}, description = "Query for region; comma separated list of regions,"
+            + " e.g.: 1:300000-400000000,15:343453463-8787665654", arity = 1)
+    public String regions;
+
+    @Parameter(names = {"--region-file"}, description = "Query for 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 = "Query for the 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 = "Query for the 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 = {"--missing-allele"}, description = "Query for the number of missing alleles of a given"
+            + " study and cohort. Use the following format enclosed with double quotes: \"study_name::cohort_name"
+            + "[<|>|<=|>=|==|!=]value\", e.g.: \"1000g::all==5\"", arity = 1)
+    public String missingAlleles;
+
+    @Parameter(names = {"--missing-genotype"}, description = "Query for the number of missing genotypes of a"
+            + " given study and cohort. Use the following format enclosed with double quotes: \"study_name::"
+            + "cohort_name[<|>|<=|>=|==|!=]value\", e.g.: \"1000g::all!=0\"", arity = 1)
+    public String missingGenotypes;
+
+    @Parameter(names = {"--ct", "--consequence-type"}, description = "Query for 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 = "Query for gene; comma separated list of gene names, e.g.:"
+            + " \"BIN3,ZNF517\"", arity = 1)
+    public String genes;
+
+    @Parameter(names = {"--clinvar"}, description = "Query for clinvar (accession); comma separated list of"
+            + " accessions", arity = 1)
+    public String clinvar;
+
+    @Parameter(names = {"--cosmic"}, description = "Query for cosmic (mutation ID); comma separated list of"
+            + " mutations IDs", arity = 1)
+    public String cosmic;
+
+//        @Parameter(names = {"--gwas"}, description = "Query for gwas (traits); comma separated list of traits",
+// arity = 1)
+//        public String gwas;
+
+    @Parameter(names = {"--conservation"}, description = "Query for 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 = "Query for 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 = "Query for alternate population"
+            + " frequency of a given study. Use the following format enclosed with double quotes:"
+            + " \"study_name::population_name[<|>|<=|>=|==|!=]frequency_value\", e.g.: \"1000g::CEU<0.4\"",
+            arity = 1)
+    public String pf;
+
+    @Parameter(names = {"--pmaf", "--population-maf"}, description = "Query for population minor allele frequency"
+            + " of a given study. Use the following the format enclosed with double quotes: \"study_name::"
+            + "population_name[<|>|<=|>=|==|!=]frequency_value\", e.g.: \"1000g::PJL<=0.25\"", arity = 1)
+    public String pmaf;
+
+    @Parameter(names = {"--sample-genotype"}, description = "Query for sample genotypes. Use the following the"
+            + " format enclosed with double quotes: \"sample_name1:genotype1,genotype;sample_name2:genotype1\","
+            + " e.g.: \"HG00112:0/0;HG23412:1/0,1/1\"", arity = 1)
+    public String sampleGenotypes;
+
+    @Parameter(names = {"--sample-filter"}, description = "Query for sample filter, i.e.: individual attributes (family, father,"
+            + " mother, sex and phenotype) and user-defined attributes from pedigree information,"
+            + "  e.g.: \"individual.sex=MALE;Eyes=Blue\"", arity = 1)
+    public String sampleFilters;
+}

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

@@ -63,14 +63,13 @@ public void execute() {
         System.out.println("r2: " + trainingSummary.r2());
     }
 
-    public LinearRegressionAnalysis(String datasetName, String studyName, String depVarName, String indepVarName) {
-        this(datasetName, studyName, depVarName, indepVarName, 10, 0.3, 0.8);
+    public LinearRegressionAnalysis(String studyId, String depVarName, String indepVarName) {
+        this(studyId, depVarName, indepVarName, 10, 0.3, 0.8);
     }
 
-    public LinearRegressionAnalysis(String datasetName, String studyName, String depVarName, String indepVarName,
+    public LinearRegressionAnalysis(String studyId, String depVarName, String indepVarName,
                                     int numIterations, double regularization, double elasticNet) {
-        this.datasetName = datasetName;
-        this.studyName = studyName;
+        super(studyId);
         this.depVarName = depVarName;
         this.indepVarName = indepVarName;
         this.numIterations = numIterations;

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

@@ -70,14 +70,13 @@ public void execute() {
         lrModel.setThreshold(bestThreshold);
     }
 
-    public LogisticRegressionAnalysis(String datasetName, String studyName, String depVarName, String indepVarName) {
-        this(datasetName, studyName, depVarName, indepVarName, 10, 0.3, 0.8);
+    public LogisticRegressionAnalysis(String studyId, String depVarName, String indepVarName) {
+        this(studyId, depVarName, indepVarName, 10, 0.3, 0.8);
     }
 
-    public LogisticRegressionAnalysis(String datasetName, String studyName, String depVarName, String indepVarName,
+    public LogisticRegressionAnalysis(String studyId, String depVarName, String indepVarName,
                                       int numIterations, double regularization, double elasticNet) {
-        this.datasetName = datasetName;
-        this.studyName = studyName;
+        super(studyId);
         this.depVarName = depVarName;
         this.indepVarName = indepVarName;
         this.numIterations = numIterations;

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

@@ -29,13 +29,12 @@ public void execute() {
         result.show(false);
     }
 
-    public PCAAnalysis(String datasetName, String studyName, String featureName) {
-        this(datasetName, studyName, featureName, 3);
+    public PCAAnalysis(String studyId, String studyName, String featureName) {
+        this(studyId, studyName, featureName, 3);
     }
 
-    public PCAAnalysis(String datasetName, String studyName, String featureName, int kValue) {
-        this.datasetName = datasetName;
-        this.studyName = studyName;
+    public PCAAnalysis(String studyId, String studyName, String featureName, int kValue) {
+        super(studyId);
         this.featureName = featureName;
         this.kValue = kValue;
     }