MODget tool created to get list of proteins associated with a type of Post Translational Modification.

Author: Luis Francisco Hernández Sánchez

Java/PathwayQuery/nbactions.xml

@@ -10,7 +10,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-classpath %classpath no.uib.pathwayquery.ProteinGraphExtractor</exec.args>
+                <exec.args>-classpath %classpath no.uib.tools.MODGet -m 00064 -o ./output.txt</exec.args>
                 <exec.executable>java</exec.executable>
             </properties>
         </action>
@@ -24,7 +24,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath no.uib.pathwayquery.ProteinGraphExtractor</exec.args>
+                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath no.uib.tools.MODGet -m 00064 -o ./output.txt</exec.args>
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
             </properties>
@@ -39,7 +39,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-classpath %classpath no.uib.pathwayquery.ProteinGraphExtractor</exec.args>
+                <exec.args>-classpath %classpath no.uib.tools.MODGet -m 00064 -o ./output.txt</exec.args>
                 <exec.executable>java</exec.executable>
             </properties>
         </action>

Java/PathwayQuery/pom.xml

@@ -59,6 +59,18 @@
             <artifactId>trove4j</artifactId>
             <version>3.0.3</version>
         </dependency>
+        
+        <dependency>
+            <groupId>commons-cli</groupId>
+            <artifactId>commons-cli</artifactId>
+            <version>1.3.1</version>
+        </dependency>
+        
+        <dependency>
+            <groupId>org.apache.httpcomponents</groupId>
+            <artifactId>httpclient</artifactId>
+            <version>4.1.1</version>
+        </dependency>
     </dependencies>
     <build>
         <plugins>

Java/PathwayQuery/src/main/java/no/uib/DB/ConnectionNeo4j.java

@@ -0,0 +1,11 @@
+package no.uib.db;
+
+import org.neo4j.driver.v1.Driver;
+
+/**
+ * @author Luis Francisco Hernández Sánchez
+ */
+public class ConnectionNeo4j {
+
+    public static Driver driver;
+}

Java/PathwayQuery/src/main/java/no/uib/db/ConnectionNeo4j.java

@@ -0,0 +1,39 @@
+/*
+ * Copyright 2017 Luis Francisco Hernández Sánchez.
+ *
+ * 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.
+ */
+package no.uib.db;
+
+/**
+ *
+ * @author Luis Francisco Hernández Sánchez
+ */
+public class CypherQueries {
+
+    public enum Queries {
+        getProteinsByPsiMod {
+            public String toString() {
+                return "MATCH (re:ReferenceEntity)<-[:referenceEntity]-(ewas:EntityWithAccessionedSequence)-[:hasModifiedResidue]->(mr)-[:psiMod]->(mod)\n"
+                        + "WHERE mod.identifier IN {modList} AND ewas.speciesName = \"Homo sapiens\"\n"
+                        + "RETURN DISTINCT re.identifier as protein";
+            }
+        },
+        getCountAllPTMs {
+            public String toString() {
+                return "MATCH path = (re:ReferenceEntity)<-[:referenceEntity]-(ewas:EntityWithAccessionedSequence)-[:hasModifiedResidue]->(mr)-[:psiMod]->(mod) \n"
+                        + "WHERE ewas.speciesName = \"Homo sapiens\" RETURN count(DISTINCT re), mod.identifier, mod.name";
+            }
+        }
+    }
+}

Java/PathwayQuery/src/main/java/no/uib/db/CypherQueries.java

@@ -1,4 +1,4 @@
-package no.uib.DB;
+package no.uib.db;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -7,18 +7,20 @@
 import java.io.FileWriter;
 import java.io.IOException;
 import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
-import no.uib.Model.Pair;
-import no.uib.Model.Reaction;
+import no.uib.model.Pair;
+import no.uib.model.Reaction;
 import no.uib.pathwayquery.Conf;
 import static no.uib.pathwayquery.ProteinGraphExtractor.G;
 import org.neo4j.driver.v1.Record;
 import org.neo4j.driver.v1.Session;
 import org.neo4j.driver.v1.StatementResult;
 import org.neo4j.driver.v1.Transaction;
 import org.neo4j.driver.v1.Values;
+import no.uib.db.CypherQueries.Queries;
 
 /**
  *
@@ -562,4 +564,22 @@ public static List<Record> getVerticesByType(Conf.EntityType t) {
         session.close();
         return result.list();
     }
+
+    public static List<String> getProteinListByMods(List<String> mods) {
+
+        String query = CypherQueries.Queries.getProteinsByPsiMod.toString();
+        mods.replaceAll(mod -> "\"" + mod + "\"");
+        query = query.replace("{modList}", mods.toString());
+        List<String> result = new ArrayList<>();
+
+        Session session = ConnectionNeo4j.driver.session();
+        StatementResult queryResult = session.run(query);
+
+        for (Record record : queryResult.list()) {
+            result.add(record.get("protein").asString());
+        }
+
+        session.close();
+        return result;
+    }
 }

Java/PathwayQuery/src/main/java/no/uib/DB/ReactomeAccess.java renamed to Java/PathwayQuery/src/main/java/no/uib/db/ReactomeAccess.java

@@ -1,4 +1,4 @@
-package no.uib.DB;
+package no.uib.db;
 
 import java.io.FileWriter;
 import java.io.InputStream;

Java/PathwayQuery/src/main/java/no/uib/DB/UniprotAccess.java renamed to Java/PathwayQuery/src/main/java/no/uib/db/UniprotAccess.java

@@ -1,4 +1,4 @@
-package no.uib.Model;
+package no.uib.model;
 
 /**
  *

Java/PathwayQuery/src/main/java/no/uib/Model/AdjacentNeighbor.java renamed to Java/PathwayQuery/src/main/java/no/uib/model/AdjacentNeighbor.java

@@ -1,4 +1,4 @@
-package no.uib.Model;
+package no.uib.model;
 
 import gnu.trove.map.hash.TObjectByteHashMap;
 

Java/PathwayQuery/src/main/java/no/uib/Model/BiMapByteString.java renamed to Java/PathwayQuery/src/main/java/no/uib/model/BiMapByteString.java

@@ -1,4 +1,4 @@
-package no.uib.Model;
+package no.uib.model;
 
 import gnu.trove.map.hash.TObjectByteHashMap;
 import java.io.UnsupportedEncodingException;