Refs #294

cpath-cli/src/main/java/cpath/analysis/LandingAndLinkout.java

@@ -0,0 +1,61 @@
+package cpath.analysis;
+
+import cpath.config.CPathSettings;
+import cpath.service.Analysis;
+import cpath.service.CPathService;
+import cpath.service.CPathUtils;
+import org.biopax.paxtools.model.Model;
+import org.biopax.paxtools.model.level3.RelationshipXref;
+import org.biopax.paxtools.model.level3.UnificationXref;
+import org.biopax.paxtools.model.level3.Xref;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.TreeSet;
+
+public class LandingAndLinkout implements Analysis<Model> {
+
+    private static final Logger LOG = LoggerFactory.getLogger(LandingAndLinkout.class);
+//    public static final String JAVA_OPTION_IDTYPE = "cpath.analysis.linkout.type";
+    private static final CPathSettings cpath = CPathSettings.getInstance();
+
+    @Autowired
+    CPathService service;
+
+    @Override
+    public void execute(Model model) {
+        //export the list of unique UniProt primary accession numbers
+        LOG.info("creating the list of primary uniprot IDs...");
+        Set<String> acs = new TreeSet<>();
+        //exclude publication xrefs
+        Set<Xref> xrefs = new HashSet<>(model.getObjects(UnificationXref.class));
+        xrefs.addAll(model.getObjects(RelationshipXref.class));
+        long left = xrefs.size();
+        for(Xref x : xrefs) {
+            String id = x.getId();
+            if (CPathUtils.startsWithAnyIgnoreCase(x.getDb(),"uniprot")
+                    && id != null && !acs.contains(id))
+                acs.addAll(service.map(id, "UNIPROT"));
+            if(--left % 10000 == 0)
+                LOG.info(left + " xrefs to map...");
+        }
+
+        PrintWriter writer;
+        try {
+            writer = new PrintWriter("uniprot.txt");
+        } catch (FileNotFoundException e) {
+            throw new RuntimeException("", e);
+        }
+        writer.println(String.format("#PathwayCommons v%s - primary UniProt accession numbers:", cpath.getVersion()));
+        for(String ac : acs)
+            writer.println(ac);
+        writer.close();
+
+        LOG.info("generated uniprot.txt");
+    }
+}