Hallo Richard, thank you for the fast response. Now I understand, what the error message means. Sorry for asking stupid questions but sometimes I don't see the wood for the trees. ;)
Cheers, Antje On Thu, 2008-03-06 at 13:29 +0000, Richard Holland wrote: > -----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----- > -- Antje Wollherr, Diplom-Bioinformatikerin Göttinger Genomlabor Institut für Mikrobiologie und Genetik Grisebachstraße 8 37077 Göttingen Email: [EMAIL PROTECTED] Tel.: 0551 393843 Fax: 0551 394195 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
