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Merge pull request #13 from P2GX/develop
Develop
2 parents 497a205 + 28047cb commit ac039ed

30 files changed

+1520
-240
lines changed

‎.gitignore‎

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hs_err_pid*
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replay_pid*
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/.idea/
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/data/
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/target/
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/candidates.tsv
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.idea/
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data/
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target/
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candidates.*
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/candidates/
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.DS_Store

‎pom.xml‎

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@@ -4,7 +4,7 @@
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<modelVersion>4.0.0</modelVersion>
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<groupId>org.monarchinitiative.hpotools</groupId>
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<artifactId>hpotools</artifactId>
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<version>0.0.9</version>
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<version>0.1.5</version>
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<packaging>jar</packaging>
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<name>hpotools</name>
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@@ -162,6 +162,16 @@
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<version>5.11.4</version> <!-- Use the latest version available -->
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-math3</artifactId>
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<version>3.6.1</version>
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</dependency>
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<dependency>
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<groupId>com.google.protobuf</groupId>
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<artifactId>protobuf-java-util</artifactId>
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<version>3.21.12</version> <!-- or compatible version -->
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</dependency>
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</dependencies>
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<build>

‎src/main/java/org/monarchinitiative/hpotools/Main.java‎

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@@ -18,13 +18,14 @@ public static void main(String[] args) {
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}
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LOGGER.trace("Starting HPO tools");
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CommandLine cline = new CommandLine(new Main())
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.addSubcommand("dist", new HpoDistCommand())
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.addSubcommand("download", new DownloadCommand())
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.addSubcommand("encoding", new EncodingCommand())
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.addSubcommand("maxo", new MaxoCommand())
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.addSubcommand("mondo", new MondoCommand())
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.addSubcommand("onset", new OnsetCommand())
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.addSubcommand("simhpo", new SimHpoCommand())
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.addSubcommand("sim", new SimHpoCommand())
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.addSubcommand("stats", new StatsCommand())
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.addSubcommand("translate", new DiseaseTranslateCommand())
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.addSubcommand("tsv", new Hpo2TsvCommand())
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.addSubcommand("word", new WordCommand())
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;

‎src/main/java/org/monarchinitiative/hpotools/analysis/HpoStats.java‎

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This file was deleted.

‎src/main/java/org/monarchinitiative/hpotools/analysis/maxo/MaxoAnnot.java‎

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package org.monarchinitiative.hpotools.analysis.maxo;
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import org.monarchinitiative.phenol.base.PhenolRuntimeException;
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import org.monarchinitiative.phenol.ontology.data.TermId;
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/**
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* disease_id
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* disease_name
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* citation
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* maxo_id
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* maxo_label
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* hpo_id
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* maxo_relation
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* evidence_code
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* extension_id
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* extension_label
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* attribute
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* creator
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* last_update
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* created_on
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*/
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public class MaxoAnnot {
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private final TermId diseaseId;
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private final String diseaseLabel;
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private final String citation;
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private final TermId maxoId;
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private final String maxoLabel;
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private final TermId hpoId;
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private final String maxoRelation;
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private final String evidenceCode;
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private final TermId extensionId;
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private final String extensionLabel;
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private final String attribute;
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private final String creator;
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private final String last_update;
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private final String created_on;
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private MaxoAnnot(TermId diseaseId,
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String diseaseLabel,
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String citation,
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TermId maxoId,
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String maxoLabel,
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TermId hpoId,
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String maxoRelation, String evidenceCode, TermId extensionId, String extensionLabel, String attribute, String creator, String lastUpdate, String createdOn) {
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this.diseaseId = diseaseId;
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this.diseaseLabel = diseaseLabel;
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this.citation = citation;
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this.maxoId = maxoId;
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this.maxoLabel = maxoLabel;
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this.hpoId = hpoId;
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this.maxoRelation = maxoRelation;
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this.evidenceCode = evidenceCode;
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this.extensionId = extensionId;
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this.extensionLabel = extensionLabel;
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this.attribute = attribute;
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this.creator = creator;
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this.last_update = lastUpdate;
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this.created_on = createdOn;
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}
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public static MaxoAnnot fromLine(String line) {
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String[] tokens = line.split("\t");
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if (tokens.length != 14) {
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throw new PhenolRuntimeException("Malformed MaxoAnnot: " + line);
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}
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TermId diseaseId = TermId.of(tokens[0]);
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String label = tokens[1];
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String citation = tokens[2];
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TermId maxoId = TermId.of(tokens[3]);
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String maxoLabel = tokens[4];
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TermId hpooId = TermId.of(tokens[5]);
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String maxoRelation = tokens[6];
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String evidenceCode = tokens[7];
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TermId extensionId = null;
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String extensionLabel = null;
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if (tokens[8] != null && tokens[8].length() > 3) {
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extensionId = TermId.of(tokens[8]);
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extensionLabel = tokens[9];
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}
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String attribute = tokens[10];
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String creator = tokens[11];
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String lastUpdate = tokens[12];
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String createdOn = tokens[13];
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return new MaxoAnnot(diseaseId,
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label,
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citation,
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maxoId,
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maxoLabel,
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hpooId,
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maxoRelation,
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evidenceCode,
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extensionId,
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extensionLabel,
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attribute,
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creator,
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lastUpdate,
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createdOn);
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}
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public TermId diseaseId() {
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return diseaseId;
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}
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public String diseaseLabel() {
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return diseaseLabel;
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}
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public String citation() {
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return citation;
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}
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public TermId maxoId() {
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return maxoId;
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}
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public String maxoLabel() {
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return maxoLabel;
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}
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public TermId hpoId() {
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return hpoId;
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}
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public String maxoRelation() {
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return maxoRelation;
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}
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public String evidenceCode() {
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return evidenceCode;
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}
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public TermId extensionId() {
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return extensionId;
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}
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public String extensionLabel() {
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return extensionLabel;
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}
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public String attribute() {
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return attribute;
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}
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public String creator() {
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return creator;
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}
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public String lastUpdate() {
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return last_update;
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}
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public String createdOn() {
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return created_on;
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}
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}

‎src/main/java/org/monarchinitiative/hpotools/analysis/maxo/MaxoDxAnnot.java‎

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package org.monarchinitiative.hpotools.analysis.maxo;
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import org.monarchinitiative.phenol.base.PhenolRuntimeException;
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import org.monarchinitiative.phenol.ontology.data.TermId;
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/**
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* hpo_id hpo_label predicate_id maxo_id maxo_label creator_id
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*/
9+
public class MaxoDxAnnot {
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private final TermId hpo_id;
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private final String hpo_label;
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private final String predicate;
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private final TermId maxo_id;
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private final String maxoLabel;
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private final String creator_id;
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public MaxoDxAnnot(TermId hpoId,
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String hpoLabel,
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String predicateId,
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TermId maxoId,
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String maxoLabel,
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String creatorId) {
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this.hpo_id = hpoId;
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this.hpo_label = hpoLabel;
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this.predicate = predicateId;
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this.maxo_id = maxoId;
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this.maxoLabel = maxoLabel;
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this.creator_id = creatorId;
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}
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public static MaxoDxAnnot fromLine(String line) {
34+
String[] fields = line.split("\t");
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if (fields.length != 6) {
36+
String e = String.format("Invalid format with %d fields (expected 5): %s",
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fields.length, line);
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throw new PhenolRuntimeException(e);
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}
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TermId hpoId = TermId.of(fields[0]);
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String hpoLabel = fields[1];
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String predicate = fields[2];
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TermId maxoId = TermId.of(fields[3]);
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String maxoLabel = fields[4];
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String creatorId = fields[5];
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return new MaxoDxAnnot(hpoId,
47+
hpoLabel,
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predicate,
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maxoId,
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maxoLabel,
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creatorId);
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}
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public TermId hpoId() {
55+
return hpo_id;
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}
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public String hpoLabel() {
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return hpo_label;
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}
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public String predicate() {
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return predicate;
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}
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public TermId maxoId() {
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return maxo_id;
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}
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public String maxoLabel() {
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return maxoLabel;
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}
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public String creatorId() {
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return creator_id;
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}
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}

‎src/main/java/org/monarchinitiative/hpotools/analysis/simhpo/IProportionalSampler.java‎

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public interface IProportionalSampler<E> {
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7-
public E sample();
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E sample();
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9-
public List<E> sample(int n);
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List<E> sample(int n);
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}

‎src/main/java/org/monarchinitiative/hpotools/analysis/simhpo/ProportionalSamplerWithReplacement.java‎

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}
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2626
public List<E> sample(int n) {
27-
List<E> selectedElements = new ArrayList<E>();
27+
List<E> selectedElements = new ArrayList<>();
2828
for (int i = 0; i < n; i++) {
2929
selectedElements.add(sample());
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}

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