Hi! What's wrong with this code:
I've got a sequence in GenBank format from ftp://ncbi.nlm.nih.gov/genbank/genomes/C_elegans/CHR_I/worm_X.gbk and tried to parse it with this code: ----------------------- import org.biojava.bio.*; import org.biojava.bio.symbol.*; import org.biojava.bio.seq.*; import org.biojava.bio.seq.io.*; import java.io.*; import java.util.*; public class TestReadingGenBankFiles { public TestReadingGenBankFiles() { } public static void main(String[] args) { try{ File GenBankFile = new File("worm_X.gbk"); System.out.println("Loading sequence..."); BufferedReader eReader = new BufferedReader( new InputStreamReader(new FileInputStream(GenBankFile))); SequenceIterator seqI = SeqIOTools.readGenbank(eReader); System.out.println("Loaded..."); System.out.println("Getting seq..."); Sequence seq = seqI.nextSequence(); System.out.println("Got "+seq.getName()); }catch(Throwable t){ t.printStackTrace();}; } } --------------------------- Though this code worked on many sequencies, here I have Loading sequence... Loaded... Getting seq... java.lang.ArrayIndexOutOfBoundsException at org.biojava.bio.seq.io.GenbankContext.hasHeaderTag(GenbankFormat.java:685) at org.biojava.bio.seq.io.GenbankContext.processHeaderLine(GenbankFormat.java:5 44) at org.biojava.bio.seq.io.GenbankContext.processFeatureLine(GenbankFormat.java: 497) at org.biojava.bio.seq.io.GenbankContext.processLine(GenbankFormat.java:364) at org.biojava.bio.seq.io.GenbankFormat.readSequence(GenbankFormat.java:137) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:100) rethrown as org.biojava.bio.BioException: Could not read sequence at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:103) at caijava.TestReadingGenBankFiles.main(TestReadingGenBankFiles.java:35) ------------------------------------- What's wrong? Is the parser could be applied to such long sequencies or there are limitations? Thanks, Andrey Zinovyev. _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
