[Biojava-l] Parsing Genbank-sequences from NCBI

[Seth Johnson]

More problems with parsing nucleotide sequences from NCBI.  Apparently,
there's an odd dbxref tag on some of the sequences submitted by ATCC that
causes an exception.  I've ran into 2 so far, but I'm sure there are more:

AA343569.1
AA325485.1

Exceptions produced are as follows:
--------------------------------------------------------------
Trying to get: AA343569.1
org.biojava.bio.BioException: Failed to read Genbank sequence
        at
org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:157)
        at exonhit.parsers.EventParser.getSeqFromNCBI(EventParser.java:250)
        at exonhit.parsers.EventParser.insertRglrSE(EventParser.java:197)
        at
exonhit.parsers.EventParser.createSpliceEvents(EventParser.java:105)
        at exonhit.parsers.EventParser.main(EventParser.java:310)
Caused by: org.biojava.bio.BioException: Could not read sequence
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112)
        at
org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:153)
        ... 4 more
Caused by: org.biojava.bio.seq.io.ParseException: Bad dbxref found: ATCC
(inhost):145151, accession:AA343569
        at
org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:438)
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
        ... 5 more
Java Result: -1
=========================================================
Trying to get: AA325485.1
org.biojava.bio.BioException: Failed to read Genbank sequence
        at
org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:157)
        at exonhit.parsers.EventParser.getSeqFromNCBI(EventParser.java:250)
        at exonhit.parsers.EventParser.insertRglrSE(EventParser.java:197)
        at
exonhit.parsers.EventParser.createSpliceEvents(EventParser.java:105)
        at exonhit.parsers.EventParser.main(EventParser.java:312)
Caused by: org.biojava.bio.BioException: Could not read sequence
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112)
        at
org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:153)
        ... 4 more
Caused by: org.biojava.bio.seq.io.ParseException: Bad dbxref found: ATCC
(inhost):125990, accession:AA325485
        at
org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:438)
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
        ... 5 more
Java Result: -1

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