Merge pull request #166 from TheJacksonLaboratory/develop

Develop

README.md

@@ -1,75 +1,23 @@
-# isopret
+# isopretGO
 
-Isoform Interpretation (isopret) is Java tool to help interpret the potential biological
-functions that are affected by differential alternative splicing. Isopret is
-available as a Java desktop application. Most users should download the latest version from the
-Releases page.
-
-
-
-## Background
-[Gene Ontology](http://geneontology.org/) traditionally has provided
-annotations for genes rather than for specific isoforms. However, in
-some cases, the functions of the individual isoforms of a gene are
-differ with respect to one or more of the gene's function. In this project,
-we have developed an algorithm for prediction of isoform-specific function
-across the entire transcriptome. The isopret app offers a number of
-ways to visualize and analyze RNA-seq datasets for Gene Ontology
-functions that are overrepresented either among the differentially
-expressed genes or the differentially spliced isoforms.
-
-## HBA-DEALS
-Isopret requires as input a file that has the fold changes and p-values
-for genes and isoforms in a case-control cohort that has been studied
-by RNA-seq. We have previously publised [HBA-DEALS](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02072-6),
-a hierarchical Bayesian algorithm that performs such an analysis, and this
-is the recommended input file.
-
-## Note to Macintosh users
-
-Isopret requires Java 17 and makes use of [JavaFX](https://openjfx.io/) to implement the
-graphical user interface (GUI). We have noticed that JavaFX GUI apps including isopret have crashed on
-Macintosh laptops with the new ARM M1 chip when using Oracle's SDK (version 17.0.2). We
-have used [Azul Zulu](https://www.azul.com/downloads/?package=jdk) JDKs on M1 Macintoshes and
-could run Isopret and other JavaFX apps without problems.
-
-We offer pre-built installation files for MacIntosh (M1 and Intel) in the Release section.
+Isoform Interpretation (isopret) with Gene Ontology (isopretGO) is Java desktop application to 
+visualize the functional implications of differential gene expression and differential alternative splicing
+in RNA-seq data. isopretGO leverages isoform-specific functional (GO) annotations presented in
+[Karlebach G, et al. (2023) Bioinformatics 39:btad132](https://pubmed.ncbi.nlm.nih.gov/36929917/)
+for an approach towards GO overrepresentation analysis of differential transcripts, and presents
+a graphicual user interface (GUI) application to perform the analysis and explore the results.
 
-## Note to Linux users
+See the [online documentation](https://thejacksonlaboratory.github.io/isopretGO/) for installation and usage instructions.
 
-The easiest way to run isopret-gui on a linux system is to run the downloadable JAR file from the releases page.
 
-```bash
-java -jar isopret-gui.jar
-```
-
-Additionally, an installation file is provided as explained in [PACKAGE](PACKAGE.md).
-
-
-### Further information
+interpret the potential biological  functions that are affected by differential alternative splicing. Isopret is
+available as a Java desktop application. Most users should download the latest version from the
+Releases page.
 
-Please see the [ReadTheDocs](https://isopret.readthedocs.io/en/latest/).
 A manuscript is in preparation.
 
 
 
-## Set up documentation
-
-Enter the following code to install mkdocs and run a server locally. The GitHub action will create a comparable site online.
-
-```
-python3 -m venv venv
-source venv/bin/activate
-pip install mkdocs
-pip install mkdocs-material
-pip install mkdocs-material[imaging]
-pip install mkdocs-material-extensions
-pip install pillow cairosvg
-pip install mkdocstrings[python]
-mkdocs serve
-```
-
-
 
 
 

docs/index.md

@@ -4,9 +4,23 @@ IsopretGO (Isoform Interpretation for Gene Ontology) leverages predictions of is
 made by the [isopret expectation maximization algorithm](https://pubmed.ncbi.nlm.nih.gov/36929917/){:target="\_blank"}.
 to perform gene-level  and isoform-level GO overrepresentation analysis.
 
-
-
-
+## Background: Gene Ontology
+[Gene Ontology](http://geneontology.org/) traditionally has provided
+annotations for genes rather than for specific isoforms. However, in
+some cases, the functions of the individual isoforms of a gene are
+differ with respect to one or more of the gene's function. In this project,
+we have developed an algorithm for prediction of isoform-specific function
+across the entire transcriptome. The isopret app offers a number of
+ways to visualize and analyze RNA-seq datasets for Gene Ontology
+functions that are overrepresented either among the differentially
+expressed genes or the differentially spliced isoforms.
+
+## Background: HBA-DEALS
+Isopret requires as input a file that has the fold changes and p-values
+for genes and isoforms in a case-control cohort that has been studied
+by RNA-seq. We have previously published [HBA-DEALS](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02072-6),
+a hierarchical Bayesian algorithm that performs such an analysis, and this
+is the recommended input file.
 Isopret uses the analysis (output) file of
 [HBA-DEALS](https://pubmed.ncbi.nlm.nih.gov/32660516/){:target="_blank"}.
 

docs/setup.md

@@ -44,5 +44,27 @@ java -jar target/isopret.jar
 
 
 
+## Set up documentation
+
+This step is not needed to run the application, but rather describes the code we use to 
+generate the isopretGO documentation.
+Enter the following code to install mkdocs and run a server with the documentation locally. 
+The GitHub action will create a comparable site online.
+
+```
+python3 -m venv venv
+source venv/bin/activate
+pip install mkdocs
+pip install mkdocs-material
+pip install mkdocs-material[imaging]
+pip install mkdocs-material-extensions
+pip install pillow cairosvg
+pip install mkdocstrings[python]
+mkdocs serve
+```
+
+
+
+
 
 

isopret-cli/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.1.17</version>
+        <version>1.1.19</version>
     </parent>
 
     <artifactId>isopret-cli</artifactId>
@@ -19,6 +19,11 @@
             <artifactId>isopret-core</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.jax.isopret</groupId>
+            <artifactId>isopret-data</artifactId>
+            <version>${project.parent.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.jax.isopret</groupId>
             <artifactId>isopret-io</artifactId>

isopret-cli/src/main/java/module-info.java

@@ -5,6 +5,8 @@
     requires org.jax.isopret.core;
     requires org.jax.isopret.io;
     requires org.monarchinitiative.phenol.analysis;
+    requires org.jax.isopret.data;
+    requires org.jax.isopret.exception;
 
     opens org.jax.isopret.cli.command to info.picocli;
 }

isopret-cli/src/main/java/org/jax/isopret/cli/command/AbstractIsopretCommand.java

@@ -1,5 +1,6 @@
 package org.jax.isopret.cli.command;
 
+import org.jax.isopret.data.Transcript;
 import org.jax.isopret.model.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

isopret-cli/src/main/java/org/jax/isopret/cli/command/GoOverrepCommand.java

@@ -4,7 +4,11 @@
 import org.jax.isopret.core.IsopretGoAnalysisRunner;
 import org.jax.isopret.core.IsopretProvider;
 import org.jax.isopret.core.analysis.IsopretStats;
-import org.jax.isopret.except.IsopretRuntimeException;
+import org.jax.isopret.data.AccessionNumber;
+import org.jax.isopret.data.GoMethod;
+import org.jax.isopret.data.MtcMethod;
+import org.jax.isopret.data.Transcript;
+import org.jax.isopret.exception.IsopretRuntimeException;
 import org.jax.isopret.model.*;
 import org.jax.isopret.core.impl.rnaseqdata.RnaSeqResultsParser;
 import org.monarchinitiative.phenol.analysis.AssociationContainer;

isopret-cli/src/main/java/org/jax/isopret/cli/command/InterproOverrepCommand.java

@@ -3,6 +3,7 @@
 import org.jax.isopret.core.*;
 import org.jax.isopret.core.impl.rnaseqdata.IsoformSpecificThresholder;
 import org.jax.isopret.core.impl.rnaseqdata.RnaSeqResultsParser;
+import org.jax.isopret.data.AccessionNumber;
 import org.jax.isopret.model.*;
 import org.jax.isopret.visualization.InterproOverrepVisualizer;
 import org.monarchinitiative.phenol.analysis.AssociationContainer;

isopret-core/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.jax.isopret</groupId>
         <artifactId>isopret</artifactId>
-        <version>1.1.17</version>
+        <version>1.1.19</version>
     </parent>
 
     <artifactId>isopret-core</artifactId>
@@ -17,6 +17,11 @@
 
 
     <dependencies>
+        <dependency>
+            <groupId>org.jax.isopret</groupId>
+            <artifactId>isopret-data</artifactId>
+            <version>${project.parent.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.monarchinitiative.phenol</groupId>
             <artifactId>phenol-annotations</artifactId>
@@ -75,9 +80,6 @@
             <scope>test</scope>
         </dependency>
 
-
-
-        <!-- https://mvnrepository.com/artifact/org.mockito/mockito-all -->
         <dependency>
             <groupId>org.mockito</groupId>
             <artifactId>mockito-all</artifactId>
@@ -91,10 +93,6 @@
             <version>5.1.1</version>
             <scope>test</scope>
         </dependency>
-
-
-
-        <!-- https://mvnrepository.com/artifact/de.charite.compbio/Jannovar -->
         <dependency>
             <groupId>de.charite.compbio</groupId>
             <artifactId>Jannovar</artifactId>
@@ -107,14 +105,11 @@
                 </exclusion>
             </exclusions>
         </dependency>
-
-        <!-- https://mvnrepository.com/artifact/de.charite.compbio/jannovar-core -->
         <dependency>
             <groupId>de.charite.compbio</groupId>
             <artifactId>jannovar-core</artifactId>
             <version>${jannovar.version}</version>
         </dependency>
-
         <dependency>
             <groupId>org.monarchinitiative.svart</groupId>
             <artifactId>svart</artifactId>
@@ -124,7 +119,6 @@
             <groupId>ch.qos.logback</groupId>
             <artifactId>logback-classic</artifactId>
         </dependency>
-
     </dependencies>
 
 

isopret-core/src/main/java/module-info.java

@@ -7,14 +7,17 @@
     requires org.apache.commons.net;
     requires org.monarchinitiative.phenol.io;
     requires guava;
+    requires org.jax.isopret.data;
+    requires org.jax.isopret.exception;
 
     exports org.jax.isopret.core.analysis;
-    exports org.jax.isopret.core.impl.go;
     exports org.jax.isopret.model;
-    exports org.jax.isopret.except;
     exports org.jax.isopret.core.impl.rnaseqdata;
     exports org.jax.isopret.visualization;
     exports org.jax.isopret.core;
     exports org.jax.isopret.core.impl.interpro;
+    //exports org.jax.isopret.core.impl.hgnc;
+    exports org.jax.isopret.core.impl.go;
+    exports org.jax.isopret.core.impl.hgnc;
 
 }

isopret-core/src/main/java/org/jax/isopret/core/GoAnalysisResults.java

@@ -1,7 +1,7 @@
 package org.jax.isopret.core;
 
-import org.jax.isopret.model.GoMethod;
-import org.jax.isopret.model.MtcMethod;
+import org.jax.isopret.data.GoMethod;
+import org.jax.isopret.data.MtcMethod;
 import org.monarchinitiative.phenol.analysis.stats.GoTerm2PValAndCounts;
 
 import java.io.File;

isopret-core/src/main/java/org/jax/isopret/core/InterproMapper.java

@@ -1,12 +1,12 @@
 package org.jax.isopret.core;
 
-import org.jax.isopret.except.IsopretRuntimeException;
+import org.jax.isopret.exception.IsopretRuntimeException;
 import org.jax.isopret.core.impl.interpro.InterproDomainDescParser;
 import org.jax.isopret.core.impl.interpro.InterproDomainParser;
-import org.jax.isopret.model.AccessionNumber;
+import org.jax.isopret.data.AccessionNumber;
 import org.jax.isopret.model.DisplayInterproAnnotation;
-import org.jax.isopret.model.InterproAnnotation;
-import org.jax.isopret.model.InterproEntry;
+import org.jax.isopret.data.InterproAnnotation;
+import org.jax.isopret.data.InterproEntry;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

isopret-core/src/main/java/org/jax/isopret/core/IsopretGoAnalysisRunner.java

@@ -2,8 +2,8 @@
 
 import org.jax.isopret.core.impl.go.DefaultIsopretGoAnalysisRunner;
 import org.jax.isopret.core.impl.rnaseqdata.RnaSeqAnalysisMethod;
-import org.jax.isopret.model.GoMethod;
-import org.jax.isopret.model.MtcMethod;
+import org.jax.isopret.data.GoMethod;
+import org.jax.isopret.data.MtcMethod;
 
 import java.io.File;
 

isopret-core/src/main/java/org/jax/isopret/core/IsopretProvider.java

@@ -1,10 +1,10 @@
 package org.jax.isopret.core;
 
 import org.jax.isopret.core.impl.DefaultIsopretProvider;
-import org.jax.isopret.model.AccessionNumber;
+import org.jax.isopret.data.AccessionNumber;
 import org.jax.isopret.model.GeneModel;
 import org.jax.isopret.model.GeneSymbolAccession;
-import org.jax.isopret.model.Transcript;
+import org.jax.isopret.data.Transcript;
 import org.monarchinitiative.phenol.analysis.AssociationContainer;
 import org.monarchinitiative.phenol.ontology.data.Ontology;
 import org.monarchinitiative.phenol.ontology.data.TermId;

isopret-core/src/main/java/org/jax/isopret/core/analysis/InterproFisherExact.java

@@ -1,8 +1,8 @@
 package org.jax.isopret.core.analysis;
 
 import org.jax.isopret.core.impl.rnaseqdata.TranscriptResultImpl;
-import org.jax.isopret.model.InterproEntry;
-import org.jax.isopret.model.AccessionNumber;
+import org.jax.isopret.data.InterproEntry;
+import org.jax.isopret.data.AccessionNumber;
 import org.jax.isopret.model.AnnotatedGene;
 import org.monarchinitiative.phenol.analysis.stats.Hypergeometric;
 import org.slf4j.Logger;

isopret-core/src/main/java/org/jax/isopret/core/analysis/InterproOverrepResult.java

@@ -1,6 +1,6 @@
 package org.jax.isopret.core.analysis;
 
-import org.jax.isopret.model.InterproEntry;
+import org.jax.isopret.data.InterproEntry;
 
 import java.util.Formatter;
 

isopret-core/src/main/java/org/jax/isopret/core/configuration/IsopretDataResolver.java

@@ -1,17 +1,14 @@
 package org.jax.isopret.core.configuration;
 
 //import org.jax.isopret.core.DownloadItem;
-import org.jax.isopret.except.IsopretRuntimeException;
+import org.jax.isopret.exception.IsopretRuntimeException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.net.MalformedURLException;
-import java.net.URL;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.List;
 import java.util.Objects;
-import java.util.Set;
 
 public class IsopretDataResolver {
 

isopret-core/src/main/java/org/jax/isopret/core/impl/DefaultIsopretProvider.java

@@ -7,6 +7,8 @@
 import org.jax.isopret.core.impl.go.TranscriptFunctionFileParser;
 import org.jax.isopret.core.InterproMapper;
 import org.jax.isopret.core.impl.jannovar.JannovarReader;
+import org.jax.isopret.data.AccessionNumber;
+import org.jax.isopret.data.Transcript;
 import org.jax.isopret.model.*;
 import org.monarchinitiative.phenol.analysis.AssociationContainer;
 import org.monarchinitiative.phenol.io.OntologyLoader;
@@ -57,7 +59,7 @@ public Ontology geneOntology() {
         if (geneOntology == null) {
             Path goPath = dataResolver.goJson();
             geneOntology = OntologyLoader.loadOntology(goPath.toFile());
-            int n_terms = geneOntology.countNonObsoleteTerms();
+            int n_terms = geneOntology.nonObsoleteTermIdCount();
             LOGGER.info("Loaded Gene Ontology json file with {} terms.", n_terms);
         }
         return geneOntology;