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Add option to return sequences from the Genbank file as a stream of sequences #870

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emckee2006 wants to merge 3 commits into from
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Add option to return sequences from the Genbank file as a stream of sequences #870

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e9fec3c
Add option to return sequences from the Genbank file as a stream of s…
emckee2006 Apr 15, 2020
4eb1c20
Merge branch 'GenbankReader_SequenceStream'
emckee2006 Apr 15, 2020
7327923
Merge branch 'upstream_master'
emckee2006 Apr 15, 2020
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60 changes: 41 additions & 19 deletions biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.stream.Stream;

/**
* Use {@link GenbankReaderHelper} as an example of how to use this class where {@link GenbankReaderHelper} should be the
Expand Down Expand Up @@ -153,35 +154,56 @@ public LinkedHashMap<String,S> process(final int max) throws IOException, Compou
}

LinkedHashMap<String,S> sequences = new LinkedHashMap<>();
@SuppressWarnings("unchecked")
int i=0;
while(true) {
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@lafita lafita Apr 22, 2020

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This is what is hanging the build. Because the stream returned is null (the file does not exist, see comment below), sequence is always null and this while loop never finishes.

The while loop is not needed anymore, simply take an action if the sequence is null.

if(max>0 && i>=max) break;
i++;
String seqString = genbankParser.getSequence(bufferedReader, 0);
//reached end of file?
if(seqString==null) break;
@SuppressWarnings("unchecked")
S sequence = (S) sequenceCreator.getSequence(seqString, 0);
genbankParser.getSequenceHeaderParser().parseHeader(genbankParser.getHeader(), sequence);

// add features to new sequence
genbankParser.getFeatures().values().stream()
.flatMap(List::stream)
.forEach(sequence::addFeature);

// add taxonomy ID to new sequence
ArrayList<DBReferenceInfo> dbQualifier = genbankParser.getDatabaseReferences().get("db_xref");
if (dbQualifier != null){
DBReferenceInfo q = dbQualifier.get(0);
sequence.setTaxonomy(new TaxonomyID(q.getDatabase()+":"+q.getId(), DataSource.GENBANK));
S sequence = getSequence();
if(null == sequence) {
break;
}

sequences.put(sequence.getAccession().getID(), sequence);
}

return sequences;
}

public Stream<S> getSequencesAsStream() {
return Stream.generate(() -> {
try {
return getSequence();
} catch (IOException | CompoundNotFoundException e) {
// TODO Auto-generated catch block
e.printStackTrace();
return null;
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@josemduarte josemduarte Apr 15, 2020

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I'd rather throw the exception forward and let the caller handle it. Returning null means all callers have to handle the null and that they lose the ability to provide a good error message.

}
});
}

private S getSequence() throws IOException, CompoundNotFoundException {
String seqString = genbankParser.getSequence(bufferedReader, 0);
//reached end of file?
if(seqString==null) {
return null;
}
@SuppressWarnings("unchecked")
S sequence = (S) sequenceCreator.getSequence(seqString, 0);
genbankParser.getSequenceHeaderParser().parseHeader(genbankParser.getHeader(), sequence);

// add features to new sequence
genbankParser.getFeatures().values().stream()
.flatMap(List::stream)
.forEach(sequence::addFeature);

// add taxonomy ID to new sequence
ArrayList<DBReferenceInfo> dbQualifier = genbankParser.getDatabaseReferences().get("db_xref");
if (dbQualifier != null){
DBReferenceInfo q = dbQualifier.get(0);
sequence.setTaxonomy(new TaxonomyID(q.getDatabase()+":"+q.getId(), DataSource.GENBANK));
}

return sequence;
}

public void close() {
try {
Expand Down
22 changes: 22 additions & 0 deletions biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Stream;

import static org.hamcrest.CoreMatchers.is;
import static org.junit.Assert.assertEquals;
Expand Down Expand Up @@ -163,6 +164,27 @@ public void testProcess() throws Exception {
assertEquals(3, dnaSequence.getAccession().getVersion().intValue());
assertTrue(genbankDNA.isClosed());
}

@Test
public void testSequenceStream() {
CheckableInputStream inStream = new CheckableInputStream(this.getClass().getResourceAsStream("/two-dnaseqs.gb"));
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@lafita lafita Apr 22, 2020

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Did you also include this file in the test resources directory? It seems not to be in this PR


GenbankReader<DNASequence, NucleotideCompound> genbankDNA
= new GenbankReader<>(
inStream,
new GenericGenbankHeaderParser<>(),
new DNASequenceCreator(DNACompoundSet.getDNACompoundSet())
);

Stream<DNASequence> seqStream = genbankDNA.getSequencesAsStream();
assertEquals(seqStream.count(),2);

assertFalse(genbankDNA.isClosed());
genbankDNA.close();
assertTrue(genbankDNA.isClosed());
assertTrue(inStream.isclosed());

}

/**
* Test the process method with a number of sequences to be read at each call.
Expand Down