[Biojava-l] Encountered a Parsing Exception on Genbank

[Cox, Greg]

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: cantey.lg@pg.com [mailto:cantey.lg@pg.com]
> Sent: Wednesday, February 27, 2002 1:28 PM
> To: biojava-l@biojava.org
> 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
> 
> 
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