Permalink
Browse files

Merge branch 'master' into develop

  • Loading branch information...
pablopareja committed Apr 25, 2012
2 parents 11f54fa + 70e54a7 commit 8250403628f1d4a5f4a1b51e76b13c9194a6880f
View
2 README
@@ -24,4 +24,4 @@ User mail-list:
http://groups.google.com/group/bio4j-user
LinkedIn group:
-http://www.linkedin.com/groups/Bio4j-3890937
+http://www.linkedin.com/groups/Bio4j-3890937
View
Binary file not shown.
Binary file not shown.
View
Binary file not shown.
@@ -0,0 +1,14 @@
+<!--
+To change this template, choose Tools | Templates
+and open the template in the editor.
+-->
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+ <head>
+ <title></title>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+ </head>
+ <body>
+ Bio4j code samples
+ </body>
+</html>
@@ -0,0 +1,14 @@
+<!--
+To change this template, choose Tools | Templates
+and open the template in the editor.
+-->
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+ <head>
+ <title></title>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+ </head>
+ <body>
+ General classes/utilities
+ </body>
+</html>
@@ -20,6 +20,8 @@
/**
*
+ * This program imports the whole Bio4j DB (as specified in the executions.xml file)
+ *
* @author Pablo Pareja Tobes <ppareja@era7.com>
*/
public class CreateWholeBio4j {
@@ -28,18 +28,11 @@
import com.era7.bioinfo.bio4jmodel.relationships.protein.ProteinInterproRel;
import com.era7.bioinfo.bio4jmodel.relationships.protein.ProteinKeywordRel;
import com.era7.bioinfo.bio4j.CommonData;
-import com.era7.bioinfo.bio4jmodel.nodes.SubcellularLocationNode;
import com.era7.bioinfo.bio4jmodel.nodes.citation.ArticleNode;
import com.era7.bioinfo.bio4jmodel.nodes.citation.SubmissionNode;
-import com.era7.bioinfo.bio4jmodel.nodes.refseq.GenomeElementNode;
-import com.era7.bioinfo.bio4jmodel.relationships.SubcellularLocationParentRel;
import com.era7.bioinfo.bio4jmodel.relationships.go.IsAGoRel;
-import com.era7.bioinfo.bio4jmodel.relationships.protein.ProteinSubcellularLocationRel;
-import com.era7.bioinfo.bio4jmodel.relationships.uniref.UniRef100MemberRel;
import com.era7.bioinfo.bio4jmodel.relationships.uniref.UniRef90MemberRel;
-import com.era7.bioinfo.bio4jmodel.util.NodeRetriever;
import java.io.IOException;
-import java.util.ArrayList;
import java.util.Iterator;
import java.util.logging.FileHandler;
import java.util.logging.Level;
@@ -49,11 +42,10 @@
import org.neo4j.graphdb.Node;
import org.neo4j.graphdb.Relationship;
import org.neo4j.graphdb.index.IndexHits;
-import org.neo4j.graphdb.index.RelationshipIndex;
import org.neo4j.kernel.EmbeddedGraphDatabase;
/**
- *
+ * Test program
* @author Pablo Pareja Tobes <ppareja@era7.com>
*/
public class GetProteinData {
@@ -39,7 +39,8 @@
import org.neo4j.kernel.impl.batchinsert.BatchInserterImpl;
/**
- *
+ * Imports Expasy Enzyme DB into Bio4j (everything but Uniprot associations which are imported
+ * from Uniprot xml files.
* @author Pablo Pareja Tobes <ppareja@era7.com>
*/
public class ImportEnzymeDB implements Executable {
@@ -43,7 +43,7 @@
import org.neo4j.kernel.impl.batchinsert.BatchInserterImpl;
/**
- *
+ * Imports the Gene Ontology into Bio4j
* @author Pablo Pareja Tobes <ppareja@era7.com>
*/
public class ImportGeneOntology implements Executable {
@@ -28,7 +28,7 @@
import org.neo4j.graphdb.Transaction;
/**
- *
+ * Imports NCBI taxonomy into Bio4j
* @author Pablo Pareja Tobes <ppareja@era7.com>
*/
public class ImportNCBITaxonomy implements Executable {
@@ -72,7 +72,7 @@ public static void main(String[] args) {
File namesDumpFile = new File(args[1]);
logger.log(Level.INFO, "creating manager...");
- manager = new Bio4jManager(args[2]);
+ manager = new Bio4jManager(args[2], true, false);
NodeRetriever nodeRetriever = new NodeRetriever(manager);
@@ -31,7 +31,7 @@
import org.neo4j.kernel.impl.batchinsert.BatchInserterImpl;
/**
- *
+ * Imports RefSeq complete release into Bio4j
* @author Pablo Pareja Tobes <ppareja@era7.com>
*/
public class ImportRefSeq implements Executable {
@@ -44,7 +44,7 @@
import org.neo4j.kernel.impl.batchinsert.BatchInserterImpl;
/**
- * Imports every uniref(100,90,50) cluster info into Bio4j
+ * Imports uniref(100,90,50) clusters info into Bio4j
* @author Pablo Pareja Tobes <ppareja@era7.com>
*/
public class ImportUniref implements Executable {
@@ -25,7 +25,7 @@
import org.neo4j.kernel.impl.batchinsert.BatchInserterImpl;
/**
- *
+ * Indexes NCBI taxonomy elements by GI (gene identifiers) as specified in the official mapping file
* @author Pablo Pareja Tobes <ppareja@era7.com>
*/
public class IndexNCBITaxonomyByGiId implements Executable {
@@ -39,7 +39,7 @@
import org.neo4j.kernel.impl.batchinsert.BatchInserterImpl;
/**
- *
+ * Inits Bio4j DB and stores basic/general nodes and relationships
* @author Pablo Pareja Tobes <ppareja@era7.com>
*/
public class InitBio4jDB implements Executable {
@@ -25,7 +25,7 @@
import java.util.logging.SimpleFormatter;
/**
- *
+ * Uploads the sequences of the genome elements found in RefSeq complete release
* @author Pablo Pareja Tobes <ppareja@era7.com>
*/
public class UploadRefSeqSequencesToS3 implements Executable {
@@ -0,0 +1,14 @@
+<!--
+To change this template, choose Tools | Templates
+and open the template in the editor.
+-->
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+ <head>
+ <title></title>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+ </head>
+ <body>
+ Bio4j importing process programs/modules
+ </body>
+</html>

0 comments on commit 8250403

Please sign in to comment.