[Biojava-l] Error when parsing genbank files

Hedwig Kurka kurka at mikro.biologie.tu-muenchen.de
Tue Sep 25 12:07:22 UTC 2012


Dear Mailing-List,

I have a problem parsing genbank-files. First: I know my parser works,
because I used it several times. But for some files I get the following
error:

org.biojava.bio.BioException: Could not read sequence
.
.
.
Caused by: org.biojava.bio.seq.io.ParseException:

A Exception Has Occurred During Parsing.
Please submit the details that follow to biojava-l at biojava.org or post a
bug report to http://bugzilla.open-bio.org/

Format_object=org.biojavax.bio.seq.io.GenbankFormat
Accession=null
Id=null
Comments=Bad locus line
Parse_block=LOCUS   ABCD01000001;          10777 bp    linear          
genomic DNA
23-AUG-2012
Stack trace follows ....


        at
org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:315)
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
        ... 3 more

The Locus line in the genbank file is the following:
LOCUS       ABCD01000001;          10777 bp    linear           genomic DNA
            23-AUG-2012

Can you tell me, what Biojava expects in that line or what is too much
or missing?
I use biojava 1.82

Thanks already for helping.



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