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
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