-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 The error message says it all:
Comments=Unable to handle contig assemblies just yet BioJava does not yet support EMBL contig files such as AL009126. cheers, Richard Antje Wollherr wrote: > Hello biojava people, > > I am new to this list and also not very familiar with BioJava. I was > trying to parse an EMBL File and extract the dna sequence with > RichSequence.IOTools.readEMBLDNA(br, ns); . > > For most of the embl files this isn't a problem, but the file with > accssion number AL009126 (Bacillus subtilis 168) caused an BioExcpetion > saying the sequence could not be read. > > Can somebody tell where the problem is or how it can be solved? > I'm using BioJava 1.5. > > Thank you a lot > > Antje > > Here is the error message: > > 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.EMBLFormat > Accession=AL009126 > Id=not set > Comments=Unable to handle contig assemblies just yet > Parse_block= > Stack trace follows .... > > > at org.biojavax.bio.seq.io.EMBLFormat.readSection(EMBLFormat.java:730) > at > org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:284) > at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) > ... 2 more > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > - -- Richard Holland (BioMart) EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK Tel. +44 (0)1223 494416 http://www.biomart.org/ http://www.biojava.org/ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHz/G64C5LeMEKA/QRAn5tAJ9i3ocloh8HoPXW2BP4sINhkV1+jgCff44m DJIY1k+vicFOMoX4GCwdwGs= =8JwO -----END PGP SIGNATURE----- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
