[Biojava-l] Genbank parsing problem

[Simon Foote]

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