Hi Simon, I think I've been bitten by something like this in SwissProt files (initiation at 0?). I'll have a dig arround in the simple feature constructor and see if it is handling fuzzies correctly.
Matthew Simon Foote wrote: > 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) > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
