Hi, I'm parsing the feature table in an embl file to retrieve the information under feature key CDS. For instance, I am calculating the number of exons, the length of the exons, retrieving the protein sequence and id etc. Sometimes an IllegalArgumentException is thrown by the code sequence = seqIterator.nextSequence(); //(see below in this email)
I guess there is some problem in the embl file with the Location, so that the Sequence cannot be instantiated, and as a result these sequences will not be present in my resulting output file. Why is this exception thrown and is there any way to avoid or handle this problem? Please bear in mind that I am new to BioJava and therefore would greatly appreciate a more detailed explanation. Thanks! /Anna The code and the exceptions that are thrown are as follows: .... private Sequence sequence; .... SequenceIterator seqIterator = SeqIOTools.readEmbl (bufferedReader); SequenceIterator seqIterator = SeqIOTools.readEmbl (bufferedReader); while (seqIterator.hasNext()){ try{ sequence = seqIterator.nextSequence(); } catch (BioException e){ e.printStackTrace(); } catch (NoSuchElementException e){ e.printStackTrace(); } .... java.lang.IllegalArgumentException: Location [1045891,1046196] is outside 1..1000000 at org.biojava.bio.seq.impl.SimpleFeature.<init>(SimpleFeature.java:306) at org.biojava.bio.seq.impl.SimpleStrandedFeature.<init>(SimpleStrandedFeature. java:74) at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstruc torAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:274) at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeature Realizer.java:138) rethrown as org.biojava.bio.BioException: Couldn't realize feature at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeature Realizer.java:144) at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealiz er.java:94) at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:1 98) at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:20 4) at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase. java:168) at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilde r.java:87) at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFil ter.java:98) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:101) at EmblFileParser.<init>(EmblFileParser.java:34) at EmblToExintFormat.main(EmblToExintFormat.java:57) -------------------------------------------- Anna Henricson, MSc, PhD student Center for Genomics and Bioinformatics (CGB) Karolinska Institutet S-171 77 Stockholm Sweden Phone: +46 (0)8 524 87296 Fax: +46 (0)8 337983 _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l