I've recently run across a problem with parsing of Genbank files
containing unbounded locations.
Anyone have any idea what's causing it. I tried to trace it back
through but got lost. But I think it has to do with the single <1 for
the -35_signal as shown in the example.
Thanks,
Simon Foote
example: accession M28521
...
FEATURES Location/Qualifiers
source 1..1136
/organism="Staphylococcus aureus"
/strain="RN4220"
/db_xref="taxon:1280"
gene <1..1126
/gene="entD"
-35_signal <1
/gene="entD"
...
It throws the following errors:
java.lang.reflect.InvocationTargetException
at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown
Source)
at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:274)
at
org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:138)
at
org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:94)
at
org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:194)
at
org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:200)
at
org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:157)
at
org.biojava.bio.seq.io.SimpleSequenceBuilder.makeSequence(SimpleSequenceBuilder.java:83)
at
org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:98)
at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:101)
at GenbankToFaa.runProteinParser(GenbankToFaa.java:85)
at ParseGenbank.main(ParseGenbank.java:84)
Caused by: java.lang.IllegalArgumentException: Location [<1] is outside
1..1136
at
org.biojava.bio.seq.impl.SimpleFeature.<init>(SimpleFeature.java:282)
at
org.biojava.bio.seq.impl.SimpleStrandedFeature.<init>(SimpleStrandedFeature.java:73)
... 13 more
rethrown as org.biojava.bio.BioException: Couldn't realize feature
at
org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:140)
at
org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:94)
at
org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:194)
at
org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:200)
at
org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:157)
rethrown as org.biojava.bio.BioError: Couldn't create feature
at
org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:163)
at
org.biojava.bio.seq.io.SimpleSequenceBuilder.makeSequence(SimpleSequenceBuilder.java:83)
at
org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:98)
at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:101)
at GenbankToFaa.runProteinParser(GenbankToFaa.java:85)
at ParseGenbank.main(ParseGenbank.java:84)
--
Bioinformatics Specialist
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561 [F] 613-952-9092
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