Github issue 843 - Genebank parser (#919)

MaxGreil · web-flow · commit 4d1cf58837ca · 2021-03-26T15:58:30.000-07:00
* Github issue 843

* Changes

* Add transl_except to parser

* Test

* Test changes
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
@@ -222,7 +222,8 @@ private void parseFeatureTag(List<String[]> section) {
 					Qualifier q = new Qualifier(key, val.replace('\n', ' '));
 					gbFeature.addQualifier(key, q);
 				} else {
-					if (key.equalsIgnoreCase("translation")) {
+					if (key.equalsIgnoreCase("translation") || key.equals("anticodon")
+							|| key.equals("transl_except")) {
 						// strip spaces from sequence
 						val = val.replaceAll("\\s+", "");
 						Qualifier q = new Qualifier(key, val);
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
@@ -36,10 +36,7 @@
 import org.slf4j.LoggerFactory;
 
 import java.io.*;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 import static org.hamcrest.CoreMatchers.is;
 import static org.junit.Assert.*;
@@ -333,6 +330,35 @@ public void readSequenceWithZeroSpanFeature() throws IOException, CompoundNotFou
 		assertEquals(Strand.NEGATIVE, fLocation.getStrand());
 	}
 
+	/**
+	 * Biojava fails to parse anticodon and transl_except feature qualifiers when they line wrap.
+	 * https://github.com/biojava/biojava/issues/843
+	 */
+	@Test
+	public void testGithub843() throws Exception {
+		CheckableInputStream inStream = new CheckableInputStream(this.getClass().getResourceAsStream("/NC_018080.gb"));
+		assertNotNull(inStream);
+
+		GenbankReader<DNASequence, NucleotideCompound> genbankDNA
+				= new GenbankReader<>(
+				inStream,
+				new GenericGenbankHeaderParser<>(),
+				new DNASequenceCreator(DNACompoundSet.getDNACompoundSet())
+		);
+
+		LinkedHashMap<String, DNASequence> dnaSequences = genbankDNA.process();
+		assertNotNull(dnaSequences);
+
+		DNASequence dna = new ArrayList<>(dnaSequences.values()).get(0);
+		assertNotNull(dna);
+
+		FeatureInterface<AbstractSequence<NucleotideCompound>, NucleotideCompound> tRNAFeature = dna.getFeaturesByType("tRNA").get(0);
+		String anticodon = tRNAFeature.getQualifiers().get("anticodon").get(0).getValue();
+		assertEquals("(pos:complement(1123552..1123554),aa:Leu,seq:caa)", anticodon);
+		String transl_except = tRNAFeature.getQualifiers().get("transl_except").get(0).getValue();
+		assertEquals("(pos:complement(1123552..1123554),aa:Leu)",transl_except);
+	}
+
 	/**
 	 * Helper class to be able to verify the closed state of the input stream.
 	 */
diff --git a/biojava-core/src/test/resources/NC_018080.gb b/biojava-core/src/test/resources/NC_018080.gb
@@ -0,0 +1,28 @@
+LOCUS       NC_018080            6402658 bp    DNA     circular CON 27-OCT-2020
+DEFINITION  Pseudomonas aeruginosa DK2
+ACCESSION
+VERSION     .0
+KEYWORDS    .
+FEATURES             Location/Qualifiers
+     source          1..6402658
+                     /organism="Pseudomonas aeruginosa DK2"
+                     /mol_type="genomic DNA"
+                     /strain="DK2"
+                     /db_xref="taxon:1093787"
+     gene            complement(1123502..1123588)
+                     /locus_tag="PADK2_RS05265"
+                     /old_locus_tag="PADK2_t29613"
+     tRNA            complement(1123502..1123588)
+                     /locus_tag="PADK2_RS05265"
+                     /old_locus_tag="PADK2_t29613"
+                     /product="tRNA-Leu"
+                     /inference="COORDINATES: profile:tRNAscan-SE:2.0.6"
+                     /note="Derived by automated computational analysis using
+                     gene prediction method: tRNAscan-SE."
+                     /anticodon=(pos:complement(1123552..1123554),aa:Leu,
+                     seq:caa)
+                     /transl_except=(pos:complement(1123552..1123554),
+                     aa:Leu)
+ORIGIN
+        1 tttaaagaga ccggcgattc tagtgaaatc gaacgggcag gtcaatttcc aaccagcgat
+//
