From d890c591e53b481d7c697f45ab2093a83120437d Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 30 Apr 2014 10:49:02 +0000
Subject: [PATCH] SSDM-85: FastaUtilities with a method to determine whether a
string is a sequence of nucleic acid codes or amino acid codes.
SVN: 31436
---
.../cisd/common/fasta/FastaUtilities.java | 88 +++++++++++++++++++
.../cisd/common/fasta/SequenceType.java | 34 +++++++
.../cisd/common/fasta/FastaUtilitiesTest.java | 73 +++++++++++++++
3 files changed, 195 insertions(+)
create mode 100644 common/source/java/ch/systemsx/cisd/common/fasta/FastaUtilities.java
create mode 100644 common/source/java/ch/systemsx/cisd/common/fasta/SequenceType.java
create mode 100644 common/sourceTest/java/ch/systemsx/cisd/common/fasta/FastaUtilitiesTest.java
diff --git a/common/source/java/ch/systemsx/cisd/common/fasta/FastaUtilities.java b/common/source/java/ch/systemsx/cisd/common/fasta/FastaUtilities.java
new file mode 100644
index 00000000000..6d79e381033
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/fasta/FastaUtilities.java
@@ -0,0 +1,88 @@
+/*
+ * Copyright 2014 ETH Zuerich, SIS
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.fasta;
+
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import ch.systemsx.cisd.common.utilities.Counters;
+
+/**
+ * Utility methods for FASTA files.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class FastaUtilities
+{
+ /**
+ * Nucleic acid codes as used in FASTA files (see https://en.wikipedia.org/wiki/FASTA_format).
+ */
+ public static final List<Character> NUCLEIC_ACID_CODES = Arrays.asList('A', 'C', 'G', 'T', 'U', 'R', 'Y',
+ 'K', 'M', 'S', 'W', 'B', 'D', 'H', 'V', 'N', 'X', '-');
+
+ /**
+ * Amino acid codes as used in FASTA files (see https://en.wikipedia.org/wiki/FASTA_format).
+ */
+ public static final List<Character> AMINO_ACID_CODES = Arrays.asList('A', 'B', 'C', 'D', 'E', 'F', 'G', 'H',
+ 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'Y', 'Z', 'X', '*', '-');
+
+ private static final Set<Character> NUCLEIC_ACID_CODES_SET = new HashSet<Character>(NUCLEIC_ACID_CODES);
+ private static final Set<Character> AMINO_ACID_CODES_SET = new HashSet<Character>(AMINO_ACID_CODES);
+
+ /**
+ * Determines the sequence type from the specified line of a FASTA file.
+ *
+ * @param line Line from a FASTA file. Can be in lowercase.
+ * @throws IllegalArgumentException if the line contains a character which isn't neither
+ * from NUCLEIC_ACID_CODES nor AMINO_ACID_CODES.
+ */
+ public static SequenceType determineSequenceType(String line)
+ {
+ Counters<Character> counters = new Counters<Character>();
+ for (char c : line.toUpperCase().toCharArray())
+ {
+ boolean isNucleicAcidCode = NUCLEIC_ACID_CODES_SET.contains(c);
+ boolean isAmoniAcidCode = AMINO_ACID_CODES_SET.contains(c);
+ if (isNucleicAcidCode == false && isAmoniAcidCode == false)
+ {
+ throw new IllegalArgumentException("Invalid symbol '" + c + "' in line '" + line + "'.");
+ }
+ if (isNucleicAcidCode == false)
+ {
+ return SequenceType.PROT;
+ }
+ counters.count(c);
+ }
+ if (counters.getNumberOfDifferentObjectsCounted() > 5 || containsUAndT(counters))
+ {
+ return SequenceType.PROT;
+ }
+ int nonCommonNucleicAcidCodeSites = line.length();
+ for (Character c : "ACGTUN".toCharArray())
+ {
+ nonCommonNucleicAcidCodeSites -= counters.getCountOf(c);
+ }
+ return nonCommonNucleicAcidCodeSites == 0 ? SequenceType.NUCL : SequenceType.PROT;
+ }
+
+ private static boolean containsUAndT(Counters<Character> counters)
+ {
+ return counters.getCountOf('T') > 0 && counters.getCountOf('U') > 0;
+ }
+}
diff --git a/common/source/java/ch/systemsx/cisd/common/fasta/SequenceType.java b/common/source/java/ch/systemsx/cisd/common/fasta/SequenceType.java
new file mode 100644
index 00000000000..279b61d5fec
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/fasta/SequenceType.java
@@ -0,0 +1,34 @@
+/*
+ * Copyright 2014 ETH Zuerich, SIS
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.fasta;
+
+/**
+ * Enum of sequence types.
+ *
+ * @author Franz-Josef Elmer
+ */
+public enum SequenceType
+{
+ /**
+ * Nucleic acid sequence
+ */
+ NUCL,
+ /**
+ * Amino acid sequence
+ */
+ PROT;
+}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/fasta/FastaUtilitiesTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/fasta/FastaUtilitiesTest.java
new file mode 100644
index 00000000000..e9b611ce039
--- /dev/null
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/fasta/FastaUtilitiesTest.java
@@ -0,0 +1,73 @@
+/*
+ * Copyright 2014 ETH Zuerich, SIS
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.fasta;
+
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class FastaUtilitiesTest extends AssertJUnit
+{
+
+ @Test
+ public void testLineWithInvalidCharacter()
+ {
+ try
+ {
+ FastaUtilities.determineSequenceType("ABC3DEF");
+ } catch (IllegalArgumentException ex)
+ {
+ assertEquals("Invalid symbol '3' in line 'ABC3DEF'.", ex.getMessage());
+ }
+ }
+
+ @Test
+ public void testLineWithExclusiveAminoAcidCodes()
+ {
+ assertEquals(SequenceType.PROT, FastaUtilities.determineSequenceType("abij"));
+ }
+
+ @Test
+ public void testLineWithMoreThanFiveDifferentCodes()
+ {
+ assertEquals(SequenceType.PROT, FastaUtilities.determineSequenceType("ABCDEFG"));
+ }
+
+ @Test
+ public void testLineWithMoreUAndT()
+ {
+ assertEquals(SequenceType.PROT, FastaUtilities.determineSequenceType("UT"));
+ }
+
+ @Test
+ public void testLineWithOnlyNuclCodesWithT()
+ {
+ assertEquals(SequenceType.NUCL, FastaUtilities.determineSequenceType("AAGGCCTTN"));
+ }
+
+ @Test
+ public void testLineWithOnlyNuclCodesWithU()
+ {
+ assertEquals(SequenceType.NUCL, FastaUtilities.determineSequenceType("aagcunnau"));
+ }
+
+}
--
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