[Biojava-l] [biojavax] EMBL parser error

[Morgane THOMAS-CHOLLIER]

Hello,

I am currently using biojavax that I checked out today from CVS to parse 
an EMBL file, exported from EBI SRS server.

I ran into this error :

Exception in thread "main" org.biojava.bio.BioException: Could not read 
sequence
    at 
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:111)
    at 
org.embnet.be.biojavax.tryout.EMBLParseTest.main(EMBLParseTest.java:34)
Caused by: org.biojava.bio.seq.io.ParseException: Bad date type found: 86
    at 
org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:278)
    at 
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:108)
    ... 1 more

The EMBL file is :

ID   DQ158013   standard; genomic DNA; VRT; 118 BP.
XX
AC   DQ158013;
XX
SV   DQ158013.1
XX
DT   19-JAN-2006 (Rel. 86, Created)
DT   19-JAN-2006 (Rel. 86, Last updated, Version 1)
XX
DE   Triturus helveticus clone Thel.b9 HOXB9 (Hoxb9) gene, partial cds.

Removing the two lines that comprise the date information resolves the 
problem.

Thanks,

Morgane.

-- 
**********************************************************
Morgane THOMAS-CHOLLIER, PHD Student
Vrije Universiteit Brussels (VUB)
Laboratory of Cell Genetics
Pleinlaan 2
1050 Brussels
Belgium