Jronn disorder scores calculation: handling sequences containing the selenocysteine (Sec) amino acid.

valasatava · valasatava · commit 0473ab692452 · 2017-04-11T12:18:36.000-07:00
Unit test: the user manually converts the stop codons symbols ("*") to the "U" symbol and Jronn is expected to handle this sequence.
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java
@@ -63,20 +63,20 @@ public final class SequenceUtil {
 	/**
 	 * Valid Amino acids
 	 */
-	public static final Pattern AA = Pattern.compile("[ARNDCQEGHILKMFPSTWYV]+",
+	public static final Pattern AA = Pattern.compile("[ARNDCQEGHILKMFPSTWYVUO]+",
 		Pattern.CASE_INSENSITIVE);
 
 	/**
 	 * inversion of AA pattern
 	 */
 	public static final Pattern NON_AA = Pattern.compile(
-		"[^ARNDCQEGHILKMFPSTWYVX]+", Pattern.CASE_INSENSITIVE);
+		"[^ARNDCQEGHILKMFPSTWYVXUO]+", Pattern.CASE_INSENSITIVE);
 
 	/**
-	 * Same as AA pattern but with two additional letters - XU
+	 * Same as AA pattern but with one additional letters - X
 	 */
 	public static final Pattern AMBIGUOUS_AA = Pattern.compile(
-		"[ARNDCQEGHILKMFPSTWYVXU]+", Pattern.CASE_INSENSITIVE);
+		"[ARNDCQEGHILKMFPSTWYVXUO]+", Pattern.CASE_INSENSITIVE);
 
 	/**
 	 * Nucleotides a, t, g, c, u
diff --git a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/JronnTest.java b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/JronnTest.java
@@ -20,11 +20,16 @@
  */
 package org.biojava.nbio.ronn;
 
+import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
+import org.biojava.nbio.core.sequence.DNASequence;
+import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.biojava.nbio.core.sequence.RNASequence;
 import org.biojava.nbio.data.sequence.FastaSequence;
 import org.biojava.nbio.ronn.Jronn.Range;
 import org.junit.Test;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
 
 
 public class JronnTest {
@@ -99,4 +104,45 @@ public void close() {
 			}
 		}
 	}
+
+	/** Test the user scenario when disorder scores are calculated over a sequence containing the selenocysteine (Sec) amino acid.
+	 *  The user has to manually convert the stop codons symbols ("*") to the "U" symbol and Jronn is expected to handle this sequence.
+	 *
+	 * @throws CompoundNotFoundException
+	 */
+
+	@Test
+	public void testStopCodons() throws CompoundNotFoundException {
+
+		// gene: DIO2, NM_001007023
+		String dnaString = "ATGGGCATCCTCAGCGTAGACTTGCTGATCACACTGCAAATTCTGCCAGTTTTTTTCTCCAACTGCCTCT" +
+				"TCCTGGCTCTCTATGACTCGGTCATTCTGCTCAAGCACGTGGTGCTGCTGTTGAGCCGCTCCAAGTCCAC" +
+				"TCGCGGAGAGTGGCGGCGCATGCTGACCTCAGAGGGACTGCGCTGCGTCTGGAAGAGCTTCCTCCTCGAT" +
+				"GCCTACAAACAGCTAAATTGTCCTCCATCAGGTTTTAGCAAAGATGGACACATTTTATGACTAGTATATG" +
+				"AAGCTTATAAAAGCAGACTACTGGTCTACTCACATTTGGATTTATGGATGGTGAAATTGGGTGAGGATGC" +
+				"CCCCAATTCCAGTGTGGTGCATGTCTCCAGTACAGAAGGAGGTGACAACAGTGGCAATGGTACCCAGGAG" +
+				"AAGATAGCTGAGGGAGCCACATGCCACCTTCTTGACTTTGCCAGCCCTGAGCGCCCACTAGTGGTCAACT" +
+				"TTGGCTCAGCCACTTGACCTCCTTTCACGAGCCAGCTGCCAGCCTTCCGCAAACTGGTGGAAGAGTTCTC" +
+				"CTCAGTGGCTGACTTCCTGCTGGTCTACATTGATGAGGCTCATCCATCAGATGGCTGGGCGATACCGGGG" +
+				"GACTCCTCTTTGTCTTTTGAGGTGAAGAAGCACCAGAACCAGGAAGATCGATGTGCAGCAGCCCAGCAGC" +
+				"TTCTGGAGCGTTTCTCCTTGCCGCCCCAGTGCCGAGTTGTGGCTGACCGCATGGACAATAACGCCAACAT" +
+				"AGCTTACGGGGTAGCCTTTGAACGTGTGTGCATTGTGCAGAGACAGAAAATTGCTTATCTGGGAGGAAAG" +
+				"GGCCCCTTCTCCTACAACCTTCAAGAAGTCCGGCATTGGCTGGAGAAGAATTTCAGCAAGAGATGAAAGA" +
+				"AAACTAGATTAGCTGGTTAA";
+
+		DNASequence dnaSequence = new DNASequence(dnaString);
+		RNASequence mRNA = dnaSequence.getRNASequence();
+		ProteinSequence protein = mRNA.getProteinSequence();
+
+		String proteinString = protein.getSequenceAsString();
+		// replace the symbol * (codon TGA) with U at amino acid
+		String proteinStringU = proteinString.replaceAll("\\*", "u");
+		FastaSequence fsequence = new FastaSequence("", proteinStringU);
+		try {
+			float[] rawProbabilityScores = Jronn.getDisorderScores(fsequence);
+		}
+		catch (Exception e) {
+			fail("Disorder scores calculation doesn't work");
+		}
+	}
 }
