Confirm Genbank parser handles new accession formats.

Author: heuermh

core/src/test/java/org/biojava/bio/seq/io/SeqIOToolsTest.java

@@ -33,6 +33,7 @@
 import org.biojava.bio.BioException;
 import org.biojava.bio.seq.Sequence;
 import org.biojava.bio.seq.SequenceIterator;
+import org.biojava.bio.seq.io.GenbankFormat;
 import org.biojava.bio.symbol.SymbolList;
 
 /**
@@ -200,7 +201,41 @@ public void testDNAReadersAndWriters()
         }
 
       }
-    
+
+    private Sequence readGenbankResource(final String resource) throws Exception {
+        Sequence sequence = null;
+        BufferedReader reader = null;
+        try {
+            reader = new BufferedReader(new InputStreamReader(getClass().getResourceAsStream(resource)));
+            sequence = SeqIOTools.readGenbank(reader).nextSequence();
+        }
+        catch (Exception e) {
+            e.printStackTrace();
+            fail(e.getMessage());
+        }
+        finally {
+            try {
+                reader.close();
+            }
+            catch (Exception e) {
+                // ignore
+            }
+        }
+        return sequence;
+    }
+
+    public void testNcbiExpandedAccessionFormats() throws Exception
+    {
+        Sequence header0 = readGenbankResource("/empty_header0.gb");
+        assertEquals("CP032762", header0.getAnnotation().getProperty(GenbankFormat.LOCUS_TAG));
+
+        Sequence header1 = readGenbankResource("/empty_header1.gb");
+        assertEquals("AZZZAA02123456789", header1.getAnnotation().getProperty(GenbankFormat.LOCUS_TAG));
+
+        Sequence header2 = readGenbankResource("/empty_header2.gb");
+        assertEquals("AZZZAA02123456789", header2.getAnnotation().getProperty(GenbankFormat.LOCUS_TAG));
+    }
+
     public void testProteinReadersAndWriters()
     {
         /******* test readFastaProtein *********/

core/src/test/java/org/biojavax/bio/seq/io/GenbankFormatTest.java

@@ -161,6 +161,27 @@ public void testReadEmptySequence() {
         assertEquals(sequence.getInternalSymbolList().length(), 0);
     }
 
+    public void testNcbiExpandedAccessionFormats() throws Exception
+    {
+        RichSequence header0 = readDNAFile("/empty_header0.gb");
+        assertEquals("CP032762", header0.getName());
+        assertTrue(header0.getCircular());
+        assertEquals("BCT", header0.getDivision());
+        assertEquals("15-OCT-2018", header0.getAnnotation().getProperty(Terms.getDateUpdatedTerm()));
+
+        RichSequence header1 = readDNAFile("/empty_header1.gb");
+        assertEquals("AZZZAA02123456789", header1.getName());
+        assertFalse(header1.getCircular());
+        assertEquals("PRI", header1.getDivision());
+        assertEquals("15-OCT-2018", header1.getAnnotation().getProperty(Terms.getDateUpdatedTerm()));
+
+        RichSequence header2 = readDNAFile("/empty_header2.gb");
+        assertEquals("AZZZAA02123456789", header2.getName());
+        assertFalse(header2.getCircular());
+        assertEquals("PRI", header2.getDivision());
+        assertEquals("15-OCT-2018", header2.getAnnotation().getProperty(Terms.getDateUpdatedTerm()));
+    }
+
     /**
      * Read a genbank file, return a RichSequence
      * @param filename name of file to read

core/src/test/resources/empty_header0.gb

@@ -0,0 +1,8 @@
+LOCUS       CP032762             5868661 bp    DNA     circular BCT 15-OCT-2018
+DEFINITION  no sequence
+ACCESSION   
+VERSION     .0
+KEYWORDS    .
+FEATURES             Location/Qualifiers
+ORIGIN
+//

core/src/test/resources/empty_header1.gb

@@ -0,0 +1,8 @@
+LOCUS       AZZZAA02123456789 9999999999 bp    DNA     linear   PRI 15-OCT-2018
+DEFINITION  no sequence
+ACCESSION   
+VERSION     .0
+KEYWORDS    .
+FEATURES             Location/Qualifiers
+ORIGIN
+//

core/src/test/resources/empty_header2.gb

@@ -0,0 +1,8 @@
+LOCUS       AZZZAA02123456789 10000000000 bp    DNA     linear   PRI 15-OCT-2018
+DEFINITION  no sequence
+ACCESSION   
+VERSION     .0
+KEYWORDS    .
+FEATURES             Location/Qualifiers
+ORIGIN
+//