I've got a fix in that will treat the missing type tag as optional. This should be backed out when NCBI releases a new version, but will get people through in the meantime. The catch is that if there's a different field missing, it will fail silently. I haven't seen any records like that; if you do please let me know.
Greg > -----Original Message----- > From: Cox, Greg [mailto:[EMAIL PROTECTED]] > Sent: Wednesday, February 27, 2002 2:15 PM > To: '[EMAIL PROTECTED]'; [EMAIL PROTECTED] > Subject: RE: [Biojava-l] Encountered a Parsing Exception on Genbank > > > This record is malformed, it's something we've seen > internally with the new > version of genbank. It's missing the TYPE tag in columns 45-53. I'd > suggest: > 1) Dummy up your record so it conforms to the Genbank spec. > 2) Comment out the body of parseLocusLinePost127() if you > don't need any > information from there. > > Greg > > > -----Original Message----- > > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] > > Sent: Wednesday, February 27, 2002 1:28 PM > > To: [EMAIL PROTECTED] > > Subject: [Biojava-l] Encountered a Parsing Exception on Genbank > > > > > > In attempting to parse the source file for Genbank accession > > number AB030903, > > the following exception was encountered. Any ideas would > be greatly > > appreciated ! > > ---------------------------------------------------------- > > > > org.biojava.bio.seq.io.ParseException: LOCUS line incorrectly > > tokenized [LOCUS AB030903 1441 bp > > linear VRT 15-AUG-2000] > > > > at > > org.biojava.bio.seq.io.GenbankContext.parseLocusLinePost127(Ge > > nbankFormat.java:611) > > > > at > > org.biojava.bio.seq.io.GenbankContext.processHeaderLine(Genban > > kFormat.java:521) > > > > at > > org.biojava.bio.seq.io.GenbankContext.processLine(GenbankForma > > t.java:372) > > > > at > > org.biojava.bio.seq.io.GenbankFormat.readSequence(GenbankForma > > t.java, Compiled Code) > > > > 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 seq.UpdatedTestGenbank.main(UpdatedTestGenbank.java, > > Compiled Code) > > > > Process exited with exit code 1. > > > > Best Regards, > > Larry Cantey > > > > > > _______________________________________________ > > 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 > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
