initial sync with additional code base for conversion of gff, interpro and eggnog

MGnifyParser/build.gradle

+buildscript {
+    repositories {
+        maven { url 'https://repo.gradle.org/gradle/libs-releases' }
+        jcenter()
+        maven { url "https://plugins.gradle.org/m2/" }
+    }
+    dependencies {
+        // Jar
+        classpath 'com.github.jengelman.gradle.plugins:shadow:4.0.4'
+        // Auto increment version
+        classpath "gradle.plugin.com.zoltu.gradle.plugin:git-versioning:3.0.3"
+        // GIT
+        classpath "org.ajoberstar:grgit:1.7.2"
+
+        classpath "org.gradle:gradle-tooling-api:3.4.1"
+    }
+}
+
+apply plugin: 'maven'
+apply plugin: 'java-library'
+// Jar
+apply plugin: "com.github.johnrengelman.shadow"
+// Auto increment version
+apply plugin: "com.zoltu.git-versioning"
+
+apply plugin: 'java'
+
+sourceCompatibility = 1.8
+targetCompatibility = 1.8
+
+repositories {
+    mavenCentral()
+    mavenLocal()
+    jcenter()
+}
+
+shadowJar {
+    baseName = 'MGnifyParser'
+    classifier = null
+    version = null
+    configurations = [project.configurations.runtimeClasspath]
+
+}
+
+jar {
+    manifest {
+        attributes 'Main-Class': 'nl.munlock.main.App'
+    }
+}
+
+artifacts {
+    archives shadowJar
+}
+
+group = 'nl.wur.ssb'
+version = '0.1.0'
+description = """MGnify module for conversion"""
+
+dependencies {
+    compile group: 'nl.wur.ssb', name: 'Conversion', version: '1.0.0'
+    compile group: 'uk.ac.ebi.ena.sequence', name: 'embl-api-ff', version: '1.1.147'
+    compile group: 'com.google.code.gson', name: 'gson', version: '2.7'
+    compile group: 'com.beust', name: 'jcommander', version: '1.64'
+    compile group: 'org.biojava', name: 'biojava-core', version: '4.0.0'
+    compile group: 'com.googlecode.json-simple', name: 'json-simple', version:'1.1.1'
+    
+    testCompile group: 'junit', name: 'junit', version: '3.8.1'
+    
+}
\ No newline at end of file

MGnifyParser/gradlew

+#!/usr/bin/env sh
+
+#
+# Copyright 2015 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
+#
+#      https://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.
+#
+
+##############################################################################
+##
+##  Gradle start up script for UN*X
+##
+##############################################################################
+
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
+
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD="maximum"
+
+warn () {
+    echo "$*"
+}
+
+die () {
+    echo
+    echo "$*"
+    echo
+    exit 1
+}
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "`uname`" in
+  CYGWIN* )
+    cygwin=true
+    ;;
+  Darwin* )
+    darwin=true
+    ;;
+  MINGW* )
+    msys=true
+    ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+        JAVACMD="$JAVA_HOME/bin/java"
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD="java"
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
+    MAX_FD_LIMIT=`ulimit -H -n`
+    if [ $? -eq 0 ] ; then
+        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+            MAX_FD="$MAX_FD_LIMIT"
+        fi
+        ulimit -n $MAX_FD
+        if [ $? -ne 0 ] ; then
+            warn "Could not set maximum file descriptor limit: $MAX_FD"
+        fi
+    else
+        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+    fi
+fi
+
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
+    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+    
+    JAVACMD=`cygpath --unix "$JAVACMD"`
+
+    # We build the pattern for arguments to be converted via cygpath
+    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+    SEP=""
+    for dir in $ROOTDIRSRAW ; do
+        ROOTDIRS="$ROOTDIRS$SEP$dir"
+        SEP="|"
+    done
+    OURCYGPATTERN="(^($ROOTDIRS))"
+    # Add a user-defined pattern to the cygpath arguments
+    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+    fi
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    i=0
+    for arg in "$@" ; do
+        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+
+        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
+            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+        else
+            eval `echo args$i`="\"$arg\""
+        fi
+        i=`expr $i + 1`
+    done
+    case $i in
+        0) set -- ;;
+        1) set -- "$args0" ;;
+        2) set -- "$args0" "$args1" ;;
+        3) set -- "$args0" "$args1" "$args2" ;;
+        4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+    esac
+fi
+
+# Escape application args
+save () {
+    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+    echo " "
+}
+APP_ARGS=`save "$@"`
+
+# Collect all arguments for the java command, following the shell quoting and substitution rules
+eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+
+exec "$JAVACMD" "$@"

MGnifyParser/gradlew.bat

+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem      https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto init
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto init
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:init
+@rem Get command-line arguments, handling Windows variants
+
+if not "%OS%" == "Windows_NT" goto win9xME_args
+
+:win9xME_args
+@rem Slurp the command line arguments.
+set CMD_LINE_ARGS=
+set _SKIP=2
+
+:win9xME_args_slurp
+if "x%~1" == "x" goto execute
+
+set CMD_LINE_ARGS=%*
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega

MGnifyParser/settings.gradle

+rootProject.name = 'MGnifyParser'

MGnifyParser/src/main/java/nl/munlock/eggnog/CommandOptions.java

+package nl.munlock.eggnog;
+
+import com.beust.jcommander.JCommander;
+import com.beust.jcommander.Parameter;
+import com.beust.jcommander.ParameterException;
+import com.beust.jcommander.Parameters;
+import life.gbol.domain.AnnotationResult;
+import nl.wur.ssb.SappGeneric.CommandOptionsGeneric;
+import nl.wur.ssb.SappGeneric.ImportProv;
+import org.apache.commons.lang.StringUtils;
+import org.apache.log4j.Logger;
+
+import java.time.LocalDateTime;
+import java.util.Arrays;
+import java.util.UUID;
+
+@Parameters(commandDescription = "Available options: ")
+public class CommandOptions extends CommandOptionsGeneric {
+    private static final Logger logger = Logger.getLogger(CommandOptions.class);
+
+    public String annotResultIRI;
+
+    @Parameter(names = {"-t", "-tool"},  description = "Which conversion tool to use, (conversion, interpro, eggnog, antismash)")
+    String tool;
+
+    @Parameter(names = {"-tsv"}, description = "MGnify TSV eggnog file")
+    String eggnogFile;
+
+    @Parameter(names = {"-v", "-version"}, description = "Version of eggnog used (name should match folder name in the database folder)")
+    String toolversion;
+
+    private String commandLine;
+    private final String repository = "https://gitlab.com/sapp/annotation/eggnog";
+
+    final String description = "Eggnog annotation module of SAPP";
+    public AnnotationResult annotResult;
+
+    @Parameter(names = "-starttime", description = "Start time of code", hidden = true)
+    private LocalDateTime starttime = LocalDateTime.now();
+
+    // TODO this is the default CommandOptions code ...
+    public CommandOptions(String args[]) throws Exception {
+        try {
+            new JCommander(this, args);
+            this.commandLine = StringUtils.join(args, " ");
+
+            if (this.help || args.length == 0)
+                throw new ParameterException("");
+
+            String[] files = new String[0];
+
+            if (this.input != null) {
+                logger.info("Loading data from file");
+                files = new String[]{this.input.get(0)};
+                this.domain = nl.wur.ssb.SappGeneric.InputOutput.Input.load(this.input);
+            }
+
+            if (this.input != null) {
+                files = new String[]{this.input.get(0)};
+            }
+
+            ImportProv origin = new ImportProv(domain, Arrays.asList(files), this.output, this.commandLine, this.tool, this.toolversion, this.repository, null, this.starttime, LocalDateTime.now());
+
+            annotResult = domain.make(AnnotationResult.class, "http://gbol.life/0.1/" + UUID.randomUUID());
+            annotResultIRI = annotResult.getResource().getURI();
+            origin.linkEntity(annotResult);
+
+        } catch (ParameterException pe) {
+            int exitCode = 64;
+            if (this.help) {
+                exitCode = 0;
+            }
+            System.out.println(pe.getMessage());
+            new JCommander(this).usage();
+            System.out.println("  * required parameter");
+            System.exit(exitCode);
+        }
+    }
+}

MGnifyParser/src/main/java/nl/munlock/eggnog/Eggnog.java

+package nl.munlock.eggnog;
+
+import life.gbol.domain.*;
+import nl.munlock.eggnog.CommandOptions;
+
+import nl.wur.ssb.RDFSimpleCon.ResultLine;
+import nl.wur.ssb.SappGeneric.GBOL.SequenceBuilder;
+import nl.wur.ssb.SappGeneric.Generic;
+import nl.wur.ssb.SappGeneric.Xrefs;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.log4j.Logger;
+import org.purl.ontology.bibo.domain.Document;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Scanner;
+import java.util.UUID;
+
+public class Eggnog  extends SequenceBuilder {
+
+    private XRefProvenance xrefProv;
+    private CommandOptions arguments;
+    private File name;
+    private final Logger logger = Logger.getLogger(Eggnog.class);
+    final UUID xrefprovID = UUID.randomUUID();
+
+    public Eggnog(String[] args) throws Exception {
+        super(null, "http://gbol.life/0.1/");
+
+        arguments = new CommandOptions(args);
+
+        this.domain = arguments.domain;
+
+        // store of the final output...
+        final File output = arguments.output;
+
+        name = new File(arguments.input.get(0));
+
+        this.rootIRI = "http://gbol.life/0.1/" + xrefprovID + "/";
+
+        xrefProv = arguments.domain.make(XRefProvenance.class, rootIRI + "XRefProv");
+
+        // xrefProv.setOrigin(arguments.annotResult);
+
+        Generic.Logger(arguments.debug);
+        // If no sequences are found the analysis is obviously skipped
+        // Everything is now from loadRDF as we have set a limit to 5.000 per
+        // analysis run...
+        parser(new File(arguments.eggnogFile));
+
+        logger.info("Results are saved in: " + arguments.output.getAbsolutePath());
+        nl.wur.ssb.SappGeneric.InputOutput.Output.save(arguments.domain, arguments.output);
+
+        arguments.domain.close();
+    }
+
+    private void parser(File file) throws Exception {
+        logger.debug("Parsing the MGnify TSV file");
+
+        // Obtain protein sequences and calculate MD5
+        Iterator<ResultLine> resultLines = domain.getRDFSimpleCon().runQuery("getProteins.txt", true).iterator();
+        HashMap<String, String> locusLookup = new HashMap<>();
+        while (resultLines.hasNext()) {
+            ResultLine resultLine = resultLines.next();
+            String iri = resultLine.getIRI("protein");
+            String locus = resultLine.getLitString("locus");
+            locusLookup.put(locus.toUpperCase(), iri);
+        }
+
+        Scanner scanner = new Scanner(file);
+
+        int annotationParsed = 0;
+        while (scanner.hasNext()) {
+            annotationParsed++;
+            if (annotationParsed % 100 == 0)
+                System.out.print("Annotations parsed: " + annotationParsed + "\r");
+
+            String line = scanner.nextLine();
+
+            if (line.startsWith("#"))
+                continue;
+
+            String[] lineArray = line.split("\t");
+
+            //#query_name
+            String query_name = lineArray[0]; // done
+            String seed_eggNOG_ortholog = lineArray[1]; // done
+            String seed_ortholog_evalue = lineArray[2]; // done
+            String seed_ortholog_score = lineArray[3]; // done
+            String best_tax_level = lineArray[4];
+            String Preferred_name = lineArray[5];
+            String GOs = lineArray[6]; // xref
+            String EC = lineArray[7]; // xref
+            String KEGG_ko = lineArray[8]; // xref
+            String KEGG_Pathway = lineArray[9]; //xref
+            String KEGG_Module = lineArray[10]; //xref
+            String KEGG_Reaction = lineArray[11]; //xref
+            String KEGG_rclass = lineArray[12]; //xref
+            String BRITE = lineArray[13]; //xref
+            String KEGG_TC = lineArray[14]; //xref
+            String CAZy = lineArray[15]; //xref
+            String BiGG_Reaction = lineArray[16]; //xref
+
+            String proteinURI = locusLookup.get(query_name);
+
+            if (proteinURI == null) {
+                throw new Exception("Null found!? for " + file);
+            }
+
+            Protein proteinRDF = arguments.domain.make(life.gbol.domain.Protein.class, proteinURI);
+
+            // System.err.println(StringUtils.join(lineArray, "\n"));
+
+            // Convert to RDF! - protein URI + seed_eggNOG_ortholog identifier
+            ProteinDomain proteinDomain = arguments.domain.make(ProteinDomain.class, proteinRDF.getResource().getURI() + "/" + seed_eggNOG_ortholog);
+
+            // Annotation result
+            AnnotationResult annotationResult = arguments.domain.make(AnnotationResult.class, arguments.annotResultIRI);
+
+            // Provenance
+            String version = "1.0-MGnify";
+            String library = "eggNOG";
+
+            life.gbol.domain.FeatureProvenance featureprov = arguments.domain.make(life.gbol.domain.FeatureProvenance.class, proteinDomain.getResource().getURI() + "/" + library + "/" + version);
+
+            nl.systemsbiology.semantics.sapp.domain.InterProScan provannot = arguments.domain.make(nl.systemsbiology.semantics.sapp.domain.InterProScan.class, proteinDomain.getResource().getURI() + "/" + library + "/" + version + "/prov"); // scoretry {
+
+            if (seed_ortholog_evalue.contains(";")) {
+                provannot.setEvalue(Double.valueOf(seed_ortholog_evalue.split(";")[1]));
+            } else {
+                provannot.setEvalue(Double.valueOf(seed_ortholog_evalue));
+            }
+
+            if (seed_ortholog_score.contains(";"))
+                provannot.setScore(Double.valueOf(seed_ortholog_score.split(";")[1]));
+            else {
+                provannot.setScore(Double.valueOf(seed_ortholog_score));
+            }
+
+            Document document = domain.make(Document.class, "https://blabla.com");
+            document.setTitle("EGNOGG BLA");
+            document.setAbstract("ABSTRACT HERE");
+            // document.setDateAccepted(LocalDate.parse("2020-11-06").atStartOfDay());
+            document.setDoi("DOI HERE");
+            provannot.setReference(document);
+
+            featureprov.setAnnotation(provannot);
+            featureprov.setOrigin(annotationResult);
+            proteinDomain.addProvenance(featureprov);
+
+            XRefProvenance xrefprov = arguments.domain.make(life.gbol.domain.XRefProvenance.class, featureprov.getResource().getURI() + "/xrefprov");
+            xrefprov.setOrigin(annotationResult);
+
+            for (String go_annotation : GOs.split(",")) {
+                if (go_annotation.length() == 0) continue;
+                XRef xref = Xrefs.create(XRef.class, arguments.domain, xrefprov,