The locus line format did change recently. See the NCBI site for details. I thought a patch made it into the BioJava code for this. Which version of BioJava are you using?
Mike > -----Original Message----- > From: David Waring [mailto:[EMAIL PROTECTED]] > Sent: Friday, January 18, 2002 5:54 PM > To: Bioperl; biojava > Subject: [Biojava-l] Writing genbank files > > > I have come across a problem with genbank files using the perl module > Bio::DB::GenBank. When I get the genbank sequence from NCBI > and write the > sequence out to in genbank format the Locus line is missing the date. > > LOCUS AC104722 24949 bp DNA linear BCT > > instead of > > LOCUS AC104722 24949 bp DNA linear BCT > 21-DEC-2001 > > which is what I get when I download the file myself. I don't > know if this > represents a problem in reading the reading the file or > writing the file. > > Why am I cross-posting this to biojava???. Well the biojava > parser dies on > such a file with a message that says that the Locus line is too short. > > Is the date a required element in the Locus line? Is there > consensus on what > constitutes correct format? Has it changed recently? > > David > > > > I also noticed that the biojava parser is very picky about > the number of > spaces; delete a few spaces between DNA and linear and it dies too. > > Exception in thread "main" > org.biojava.bio.seq.io.ParseException: LOCUS > line too > short [LOCUS AC104719 17453 bp DNA > linear BCT > 21-DE > C-2001] > at > org.biojava.bio.seq.io.GenbankContext.parseLocusLinePost127(GenbankFo > rmat.java, Compiled Code) > at > org.biojava.bio.seq.io.GenbankContext.processHeaderLine(GenbankFormat > .java, Compiled Code) > at > org.biojava.bio.seq.io.GenbankContext.processLine(GenbankFormat.java, > Compiled Code) > at > org.biojava.bio.seq.io.GenbankFormat.readSequence(GenbankFormat.java, > Compiled Code) > rethrown as org.biojava.bio.BioException: Could not > read sequence > at > org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java, C > ompiled Code) > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
