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Github issue 843 - Genebank parser #919

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Merged
josemduarte merged 5 commits into from
Mar 26, 2021
Merged

Github issue 843 - Genebank parser #919

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f70075c
Github issue 843
MaxGreil Mar 1, 2021
574a977
Changes
MaxGreil Mar 2, 2021
59bb88f
Add transl_except to parser
MaxGreil Mar 3, 2021
a52126f
Test
MaxGreil Mar 5, 2021
4881428
Test changes
MaxGreil Mar 6, 2021
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3 changes: 2 additions & 1 deletion biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
Expand Down
34 changes: 30 additions & 4 deletions biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
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Expand Up @@ -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.*;
Expand Down Expand Up @@ -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.
*/
Expand Down
28 changes: 28 additions & 0 deletions biojava-core/src/test/resources/NC_018080.gb
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Original file line number Diff line number Diff line change
@@ -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
//