Parsing exception reading sequence from GenbankRichSequenceDB
Scott Frees <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <CANCM15+qpY1KuVrVhcKynp2HxynRar-U3HyoNeYK_U8vqxwN9g@mail.gmail.com> |
Hello – I have developed an application that searches and compares g-quadruplexes within mRNA. The web application has been running without any problems on several different web servers for over a year. Suddenly, just this week, it is unable to download sequence data using GenbankRichSequenceDB – has anyone else has had this problem? We are using BioJava 1.8.1 Below is the exception trace, and the code that follows is a small test app that generates the exception. This code worked without any problems prior to Tuesday this week, and we haven't made any modification to our application. ------------------------------------------------------ org.biojava.bio.BioException: Failed to read Genbank sequence at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:163) at Tester.main(Tester.java:11) Caused by: org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:159) ... 1 more Caused by: org.biojava.bio.seq.io.ParseException: A Exception Has Occurred During Parsing. Please submit the details that follow to [email protected] or post a bug report to http://bugzilla.open-bio.org/ Format_object=org.biojavax.bio.seq.io.GenbankFormat Accession=null Id=null Comments=Bad section Parse_block=<?xml version="1.0"?> Stack trace follows .... at org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:620) at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:279) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) ... 2 more Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: -4 at java.lang.String.substring(Unknown Source) at java.lang.String.substring(Unknown Source) at org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:610) ... 4 more ----------------------------- import org.biojava.bio.BioException; import org.biojava.bio.seq.db.IllegalIDException; import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB; import org.biojavax.bio.seq.RichSequence; public class Tester { public static void main(String args[]) { String id = "NM_001110.2"; // Issue occurs with any ID GenbankRichSequenceDB ncbi = new GenbankRichSequenceDB(); try { RichSequence rs = ncbi.getRichSequence(id); System.out.println(rs.seqString()); } catch (IllegalIDException e) { e.printStackTrace(); } catch (BioException e) { e.printStackTrace(); } } } _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l