Hi all,
I am currently trying to debug a little software application which uses
BioJava's core-1.8.1.jar library because it has started to throw exceptions a
while ago.
I guess the problem is, that the GenbankLocationParser is not able to handle
"Het" entries in the features section of the GenBank/GenPept format, e.g.
Het join(bond(9),bond(125))
/heterogen="( NA, 5 )"
for database id 14719485 (http://www.ncbi.nlm.nih.gov/protein/14719485) .
Calling
new GenpeptRichSequenceDB().getRichSequence("14719485");
will result in an error message like:
Error while querying 14719485!
org.biojava.bio.BioException: Failed to read Genbank sequence
at
org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB.getRichSequence(GenpeptRichSequenceDB.java:158)
Caused by: org.biojava.bio.BioException: Could not read sequence
at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
at
org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB.getRichSequence(GenpeptRichSequenceDB.java:154)
... 2 more
Caused by: org.biojava.bio.seq.io.ParseException: Could not understand
position: bond(9
at
org.biojavax.bio.seq.io.GenbankLocationParser.parsePosition(GenbankLocationParser.java:286)
at
org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:272)
at
org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:237)
at
org.biojavax.bio.seq.io.GenbankLocationParser.parseLocation(GenbankLocationParser.java:132)
at
org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:508)
at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
... 3 more
I have checked several other database entires and none of the ones that worked
had a "Het" entry. But I also failed at 56965892, 13786715, 209156668 and
12084365. Has anybody else come across this problem or knows how to fix it?
Thanks,
Dietmar
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