Dak’s new unit test that demonstrates a problem when parsing FASTA files

biojava · Apr 19, 2017 · 9de8e36 · 9de8e36
1 parent 906eb6e
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diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java b/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
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+package org.biojava.nbio.core.fasta;
+
+import java.io.InputStream;
+import java.util.LinkedHashMap;
+
+import static org.junit.Assert.* ;
+import static org.hamcrest.CoreMatchers.* ;
+
+import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
+import org.biojava.nbio.core.sequence.io.FastaReader;
+import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
+import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
+import org.biojava.nbio.core.sequence.io.util.ClasspathResource;
+import org.junit.Test;
+
+
+public class TestFASTAReader {
+
+    @Test
+    public void testProcessAll() throws Exception {
+        ClasspathResource r = new ClasspathResource("org/biojava/nbio/core/fasta/P02768.fasta");
+        FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
+        try( InputStream inStream = r.getInputStream() ) {
+            fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+                    inStream,
+                    new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+                    new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+            LinkedHashMap<String, ProteinSequence> sequences = fastaReader.process();
+            assertThat(sequences,is(notNullValue()));
+            assertThat(sequences.size(),is(1));
+        } finally {
+            if(fastaReader != null) fastaReader.close();
+        }
+    }
+    @Test
+    public void testProcess1() throws Exception {
+        ClasspathResource r = new ClasspathResource("org/biojava/nbio/core/fasta/P02768.fasta");
+        FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
+        try( InputStream inStream = r.getInputStream() ) {
+            fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+                    inStream,
+                    new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+                    new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+            assertThat(fastaReader.process(1),is(notNullValue()));
+            assertThat(fastaReader.process(1),is(nullValue()));
+        } finally {
+            if(fastaReader != null) fastaReader.close();
+        }
+    }
+    @Test
+    public void testProcess1v2() throws Exception {
+        ClasspathResource r = new ClasspathResource("org/biojava/nbio/core/fasta/TwoSequences.fasta");
+        FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
+        try( InputStream inStream = r.getInputStream() ) {
+            fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+                    inStream,
+                    new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+                    new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+            assertThat(fastaReader.process(1),is(notNullValue()));
+            assertThat(fastaReader.process(1),is(notNullValue()));
+            assertThat(fastaReader.process(1),is(nullValue()));
+        } finally {
+            if(fastaReader != null) fastaReader.close();
+        }
+    }
+
+}
diff --git a/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/P02768.fasta b/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/P02768.fasta
@@ -0,0 +1,12 @@
+>sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2
+MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF
+EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP
+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
+FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV
+ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK
+ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR
+RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE
+QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV
+LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL
+SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV
+AASQAALGL
diff --git a/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/TwoSequences.fasta b/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/TwoSequences.fasta
@@ -0,0 +1,16 @@
+>sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2
+MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF
+EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP
+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
+FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV
+ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK
+ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR
+RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE
+QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV
+LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL
+SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV
+AASQAALGL
+>sp|P00698|LYSC_CHICK Lysozyme C OS=Gallus gallus GN=LYZ PE=1 SV=1
+MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA
+TNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG
+NGMNAWVAWRNRCKGTDVQAWIRGCRL