Merge pull request #133 from TheJacksonLaboratory/develop

Develop

.gitignore

@@ -1,4 +1,5 @@
 # Compiled class file
+target/
 *.class
 
 # Log file
@@ -11,6 +12,7 @@
 .mtj.tmp/
 
 # Package Files #
+!maven-wrapper.jar
 *.jar
 *.war
 *.nar
@@ -21,11 +23,17 @@
 
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
-/vmvt-cli.iml
-/l2o.iml
-/data/
-/l2o.html
-/l2o.bed
-/l2o.igv.txt
+
+# IDE stuff
+.idea/
+*.iml
+
+# Local data files
+data/
+
+# Local output files
+*.html
+
+# Sphinx documentation
+docs/_build/
 /dependency-reduced-pom.xml
-/L2O.html

.mvn/wrapper/MavenWrapperDownloader.java

@@ -0,0 +1,117 @@
+/*
+ * Copyright 2007-present the original author or authors.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import java.net.*;
+import java.io.*;
+import java.nio.channels.*;
+import java.util.Properties;
+
+public class MavenWrapperDownloader {
+
+    private static final String WRAPPER_VERSION = "0.5.6";
+    /**
+     * Default URL to download the maven-wrapper.jar from, if no 'downloadUrl' is provided.
+     */
+    private static final String DEFAULT_DOWNLOAD_URL = "https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/"
+        + WRAPPER_VERSION + "/maven-wrapper-" + WRAPPER_VERSION + ".jar";
+
+    /**
+     * Path to the maven-wrapper.properties file, which might contain a downloadUrl property to
+     * use instead of the default one.
+     */
+    private static final String MAVEN_WRAPPER_PROPERTIES_PATH =
+            ".mvn/wrapper/maven-wrapper.properties";
+
+    /**
+     * Path where the maven-wrapper.jar will be saved to.
+     */
+    private static final String MAVEN_WRAPPER_JAR_PATH =
+            ".mvn/wrapper/maven-wrapper.jar";
+
+    /**
+     * Name of the property which should be used to override the default download url for the wrapper.
+     */
+    private static final String PROPERTY_NAME_WRAPPER_URL = "wrapperUrl";
+
+    public static void main(String args[]) {
+        System.out.println("- Downloader started");
+        File baseDirectory = new File(args[0]);
+        System.out.println("- Using base directory: " + baseDirectory.getAbsolutePath());
+
+        // If the maven-wrapper.properties exists, read it and check if it contains a custom
+        // wrapperUrl parameter.
+        File mavenWrapperPropertyFile = new File(baseDirectory, MAVEN_WRAPPER_PROPERTIES_PATH);
+        String url = DEFAULT_DOWNLOAD_URL;
+        if(mavenWrapperPropertyFile.exists()) {
+            FileInputStream mavenWrapperPropertyFileInputStream = null;
+            try {
+                mavenWrapperPropertyFileInputStream = new FileInputStream(mavenWrapperPropertyFile);
+                Properties mavenWrapperProperties = new Properties();
+                mavenWrapperProperties.load(mavenWrapperPropertyFileInputStream);
+                url = mavenWrapperProperties.getProperty(PROPERTY_NAME_WRAPPER_URL, url);
+            } catch (IOException e) {
+                System.out.println("- ERROR loading '" + MAVEN_WRAPPER_PROPERTIES_PATH + "'");
+            } finally {
+                try {
+                    if(mavenWrapperPropertyFileInputStream != null) {
+                        mavenWrapperPropertyFileInputStream.close();
+                    }
+                } catch (IOException e) {
+                    // Ignore ...
+                }
+            }
+        }
+        System.out.println("- Downloading from: " + url);
+
+        File outputFile = new File(baseDirectory.getAbsolutePath(), MAVEN_WRAPPER_JAR_PATH);
+        if(!outputFile.getParentFile().exists()) {
+            if(!outputFile.getParentFile().mkdirs()) {
+                System.out.println(
+                        "- ERROR creating output directory '" + outputFile.getParentFile().getAbsolutePath() + "'");
+            }
+        }
+        System.out.println("- Downloading to: " + outputFile.getAbsolutePath());
+        try {
+            downloadFileFromURL(url, outputFile);
+            System.out.println("Done");
+            System.exit(0);
+        } catch (Throwable e) {
+            System.out.println("- Error downloading");
+            e.printStackTrace();
+            System.exit(1);
+        }
+    }
+
+    private static void downloadFileFromURL(String urlString, File destination) throws Exception {
+        if (System.getenv("MVNW_USERNAME") != null && System.getenv("MVNW_PASSWORD") != null) {
+            String username = System.getenv("MVNW_USERNAME");
+            char[] password = System.getenv("MVNW_PASSWORD").toCharArray();
+            Authenticator.setDefault(new Authenticator() {
+                @Override
+                protected PasswordAuthentication getPasswordAuthentication() {
+                    return new PasswordAuthentication(username, password);
+                }
+            });
+        }
+        URL website = new URL(urlString);
+        ReadableByteChannel rbc;
+        rbc = Channels.newChannel(website.openStream());
+        FileOutputStream fos = new FileOutputStream(destination);
+        fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
+        fos.close();
+        rbc.close();
+    }
+
+}

.mvn/wrapper/maven-wrapper.properties

@@ -0,0 +1,2 @@
+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.6.3/apache-maven-3.6.3-bin.zip
+wrapperUrl=https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.5.6/maven-wrapper-0.5.6.jar

CHANGELOG.rst

@@ -0,0 +1,8 @@
+=========
+Changelog
+=========
+
+------
+v0.3.0
+------
+- Adding phenopacket support

README.md

@@ -28,11 +28,6 @@ This command downloads various files and generates `data/hg38_refseq_curated.ser
 this to the data subdirectory in this project or softlink it (from 'data', enter `ln -s <path>`).
 Thus, for now, this project expects the path `data/data/refseq_curated.ser`.
 
-### LIRICAL
-Run [LIRICAL](https://github.com/TheJacksonLaboratory/LIRICAL) using only the clinical manifestations
-of the case, and output a TSV file. Consider using the 
-[PhenopacketGenerator](https://github.com/TheJacksonLaboratory/PhenopacketGenerator).
-
 ## Running svann
 
 Enter the following command to see options. The LIRICAL file is the 
@@ -42,21 +37,26 @@ it is required to also use an HPO term with the major phenotypic abnormality,
 e.g., [Abnormality of the immune system](https://hpo.jax.org/app/browse/term/HP:0002715).
 
 ```
-$ java -jar target/svann.jar
-LIRICAL to overlapping SV
-  -h, --help            Show this help message and exit.
-  -l, --lirical=<liricalFile>
-
-  -o, --out=<outname>
-  -v, --vcf=<vcfFile>
-  -V, --version         Print version information and exit.
-
+$  java -jar target/svann.jar annotate -h
+  Usage: svann annotate [-hV] [-e=<enhancerFile>] [-g=<geneCodePath>]
+                        [-j=<jannovarPath>] [-t=<hpoTermIdList>] -v=<vcfFile>
+                        [-x=<outprefix>]
+  annotate VCF file
+    -e, --enhancer=<enhancerFile>
+                               tspec enhancer file
+    -g, --gencode=<geneCodePath>
+  
+    -h, --help                 Show this help message and exit.
+    -j, --jannovar=<jannovarPath>
+                               prefix for output files (default:
+                                 data/data/hg38_refseq_curated.ser )
+    -t, --term=<hpoTermIdList> HPO term IDs (comma-separated list)
+    -v, --vcf=<vcfFile>
+    -V, --version              Print version information and exit.
+    -x, --prefix=<outprefix>   prefix for output files (default: L2O )
 ```
 
 
-We can run l2o to look for specific enhancer overlaps, e.g., for terms with
-	[Abnormal T cell morphology - HP:0002843](https://hpo.jax.org/app/browse/term/HP:0002843).
-
 
 
 # Documentation

docs/deletion.rst

@@ -0,0 +1,17 @@
+.. _rstdeletion:
+
+Deletions
+=========
+
+
+A deletion is a type of DNA variant that involves the loss of genetic material. If the loss is over 1 kb, then
+the deletion is refered to as a structural variant (Note that svanna prioritizes any deletion that is included
+in the input VCF file, even those that are shorter than 1kb). Deletions may also be refered to as a type
+of copy number variant (CNV) with copy loss.
+
+
+svanna prioritization of deletions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+todo
+

docs/index.rst

@@ -17,5 +17,5 @@ of germline variants.
    setup
    running
    BND<bndannotations>
-
+   structuralvariation
 

docs/running.rst

@@ -0,0 +1,17 @@
+.. _rstrunning:
+
+Running svanna
+##############
+
+
+Creating a VCF file
+^^^^^^^^^^^^^^^^^^^
+
+We have tested svanna with VCF files
+generated by the following programs.
+
+
+1. `pbsv <https://github.com/PacificBiosciences/pbsv>`_, an SV caller provided by Pacific Biosciences. Currently,
+pbsv calls insertions, deletions, inversions, duplications, and translocations.
+
+2. `sniffles <https://pubmed.ncbi.nlm.nih.gov/29713083/>`_,  todo...

docs/setup.rst

@@ -1,73 +1,84 @@
 .. _rstsetup:
 
-Setting up svann
+Setting up SvAnna
 ================
 
-svann is a desktop Java application that requires several external files to run.
+SvAnna is a desktop Java application that requires several external files to run.
 
 
 Prerequisites
 ~~~~~~~~~~~~~
 
-svann was written with Java version 11. If you want to
-build svann from source, then the build process described below requires
-`Git <https://git-scm.com/book/en/v2>`_ and `maven <https://maven.apache.org/install.html>`_.
+SvAnna was written with Java version 11.
+`Git <https://git-scm.com/book/en/v2>`_ and
+`Java Development Kit <https://www.oracle.com/java/technologies/javase-downloads.html>`_ version 11 or better
+are required to build SvAnna from source. Most users should download the prebuilt SvAnna files from the
+`Releases page <https://github.com/TheJacksonLaboratory/svann/releases>`_.
 
 Installation
 ~~~~~~~~~~~~
 
-Go the GitHub page of `svann <https://github.com/pnrobinson/svann>`_, and clone or download the project.
+Go the GitHub page of `SvAnna <https://github.com/TheJacksonLaboratory/svann>`_, and clone or download the project.
 Build the executable from source with maven, and then test the build. ::
 
-    $ git clone https://github.com/pnrobinson/svann
+    $ git clone https://github.com/TheJacksonLaboratory/svann
     $ cd svann
-    $ mvn package
-    $ java -jar target/svann.jar
+    $ ./mvnw package
+    $ java -jar svanna-cli/target/svanna-cli.jar
     $ Usage: <main class> [options] [command] [command options]
       Options:
         -h, --help
           display this help message
       (...)
 
-
-
-svann requires `maven <https://maven.apache.org/>`_ version 3.5.3.
-
-
-Prebuilt svann executable
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Prebuilt SvAnna executable
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Alternatively, go to the `Releases section <https://github.com/pnrobinson/svann/releases>`_ on the
-svann GitHub page and download the latest precompiled version of svann.
+SvAnna GitHub page and download the latest precompiled version of SvAnna.
 
 
 The download command
 ~~~~~~~~~~~~~~~~~~~~
 
 .. _rstdownload:
 
-svann requires four additional files to run. TODO update this list!
+SvAnna requires four additional files to run. TODO update this list!
 
 1. ``hp.obo``. The main Human Phenotype Ontology file
 2. ``phenotype.hpoa`` The main annotation file with all HPO disease models
 3. ``Homo_sapiens_gene_info.gz`` A file from NCBI Entrez Gene with information about human genes
 4. ``mim2gene_medgen`` A file from the NCBI medgen project with OMIM-derived links between genes and diseases
 
-svann offers a convenience function to download all four files
-to a local directory. By default, svann will download all four files into a newly created subdirectory
+SvAnna offers a convenience function to download all four files
+to a local directory. By default, SvAnna will download all four files into a newly created subdirectory
 called ``data`` in the current working directory. You can change this default with the ``-d`` or ``--data`` options
-(If you change this, then you will need to pass the location of your directory to all other svann commands
+(If you change this, then you will need to pass the location of your directory to all other SvAnna commands
 using the ``-d`` flag). Download the files automatically as follows. ::
 
-    $ java -jar svann.jar download
+    $ java -jar svanna-cli.jar download
 
-svann will not download the files if they are already present unless the ``--overwrite`` argument is passed. For
+SvAnna will not download the files if they are already present unless the ``-f`` or ``--force-overwrite`` argument is passed. For
 instance, the following command would download the four files to a directory called datafiles and would
 overwrite any previously downloaded files. ::
 
-    $ java -jar svann.jar download -d datafiles --overwrite
+    $ java -jar svanna-cli.jar download -d datafiles --force-overwrite
 
 
 If desired, you can download these files on your own but you need to place them all in the
-same directory to run svann.
+same directory to run SvAnna.
+
+DGV: Database of Genomic Variants
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+SvAnna is being extended to filter variants for overlap with population variants. For now, SvAnna uses a downloaded
+file from the DGV (http://dgv.tcag.ca/dgv/app/downloads). Choose the file for the correct genome assembly (probably hg38), and
+download it. We then need to index this file with `tabix <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042176/>`_.
+Assuming we have downloaded the file ``GRCh38_hg38_variants_2020-02-25.txt`` from DGV, proceed with the following steps  ::
+
+    $ bgzip GRCh38_hg38_variants_2020-02-25.txt
+    $ tabix --skip-lines 1 -s 2 -b 3 -e 4 GRCh38_hg38_variants_2020-02-25.txt.gz
+
+After running the commands, the DGV file is compressed and indexed for quick random access.
+
 

docs/structuralvariation.rst

@@ -0,0 +1,22 @@
+.. _rstsv:
+
+Structural variation
+####################
+
+Structural variation (SV) is generally defined as a region of DNA approximately 1 kb and larger in size
+(`Freeman et al., 2006 <https://pubmed.ncbi.nlm.nih.gov/16809666/>`_). SV includes
+inversions and balanced translocations or genomic imbalances (insertions and deletions),
+often referred to as copy number variants (CNVs).
+
+svanna is intended to be used to annotate and interpret VCF files representing the results of
+long-read genome sequencing using approaches for calling SVs. Currently, svanna supports the
+following types of SV.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   deletion
+
+
+