[Biojava-l] Parsing Genbank-sequences from NCBI
Seth Johnson
johnson.biotech at gmail.com
Fri Aug 4 20:05:57 UTC 2006
Hi David,
I compiled my biojava.jar on 7/28 and, just to make sure, I've updated my
biojava-live cvs just now and it doesn't look like there were any changes
made since that date. The SimpleDocRef.java was last updated on 7/18 and
the version that I have does include the second constructor with 2
parameters. It seems to be related to null TITLE since all of the entries
are missing it, but I was also under the impression that null TITLE issue
was fixed. That's what is so puzzling about this. Below is the list of the
problem accession IDs if you'd like to replicate the exception:
NM_006145
NM_000602
NM_006226
NM_000371
NM_019072
NM_017884
NM_022107
NM_031418
NM_030809
NM_032731
NM_001029888
NM_001029869
NM_182572
On 8/4/06, David Scott <david at autohandle.com> wrote:
>
> hi seth-
>
> the 3rd argument to SimpleDocRef constructor is the REFERENCE title -
> which appears to be null in the trace - which happens, but rarely. i had
> the exact same problem recently - and richard put in code to check for a
> null title and then call a special 2 argument constructor for
> SimpleDocRef - any chance you don't have that code checked out?
>
> best-
> david
>
> Seth Johnson wrote:
> > Hi Richard,
> >
> >
> > I'm back for more help. I've just completed getting and parsing the
> entire
> > human genome RefSeq list from NCBI. I'm not going to post my source
> code
> > since the invoking code has been described by the gentlemen who started
> the
> > original thread last month. The result of the parsing is such that out
> of
> > ~28K sequences, 13 produced the exceptions below. I've used the latest
> > biojava code from CVS, not quite sure what the problem is on these 13.
> >
> >
> >
> > Trying to get: NM_006145
> >
> > org.biojava.bio.BioException: Failed to read Genbank sequence
> >
> > at
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(
> > GenbankRichSequenceDB.java:157)
> >
> > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java
> :162)
> >
> > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146)
> >
> > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195)
> >
> > 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)
> >
> > ... 3 more
> >
> > Caused by: java.lang.IllegalArgumentException: Could not find
> constructor
> > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class
> > java.lang.String,null)
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:78)
> >
> > at org.biojavax.RichObjectFactory.getObject(
> RichObjectFactory.java
> > :104)
> >
> > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(
> > GenbankFormat.java:387)
> >
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >
> > ... 4 more
> >
> > Caused by: java.lang.NullPointerException
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:59)
> >
> > ... 7 more
> >
> > org.biojava.bio.BioException: Failed to read Genbank sequence
> >
> > at
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(
> > GenbankRichSequenceDB.java:157)
> >
> >
> --------------------------------------------------------------------------------
> >
> > Trying to get: NM_000602
> >
> > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java
> :162)
> >
> > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146)
> >
> > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195)
> >
> > 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)
> >
> > ... 3 more
> >
> > Caused by: java.lang.IllegalArgumentException: Could not find
> constructor
> > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class
> > java.lang.String,null)
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:78)
> >
> > at org.biojavax.RichObjectFactory.getObject(
> RichObjectFactory.java
> > :104)
> >
> > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(
> > GenbankFormat.java:387)
> >
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >
> > ... 4 more
> >
> > Caused by: java.lang.NullPointerException
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:59)
> >
> > ... 7 more
> >
> >
> -------------------------------------------------------------------------------
> >
> > Trying to get: NM_006226
> >
> > org.biojava.bio.BioException: Failed to read Genbank sequence
> >
> > at
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(
> > GenbankRichSequenceDB.java:157)
> >
> > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java
> :162)
> >
> > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146)
> >
> > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195)
> >
> > 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)
> >
> > ... 3 more
> >
> > Caused by: java.lang.IllegalArgumentException: Could not find
> constructor
> > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class
> > java.lang.String,null)
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:78)
> >
> > at org.biojavax.RichObjectFactory.getObject(
> RichObjectFactory.java
> > :104)
> >
> > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(
> > GenbankFormat.java:387)
> >
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >
> > ... 4 more
> >
> > Caused by: java.lang.NullPointerException
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:59)
> >
> > ... 7 more
> >
> >
> ----------------------------------------------------------------------------------
> >
> > Trying to get: NM_000371
> >
> > org.biojava.bio.BioException: Failed to read Genbank sequence
> >
> > at
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(
> > GenbankRichSequenceDB.java:157)
> >
> > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java
> :162)
> >
> > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146)
> >
> > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195)
> >
> > 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)
> >
> > ... 3 more
> >
> > Caused by: java.lang.IllegalArgumentException: Could not find
> constructor
> > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class
> > java.lang.String,null)
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:78)
> >
> > at org.biojavax.RichObjectFactory.getObject(
> RichObjectFactory.java
> > :104)
> >
> > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(
> > GenbankFormat.java:387)
> >
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >
> > ... 4 more
> >
> > Caused by: java.lang.NullPointerException
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:59)
> >
> > ... 7 more
> >
> >
> --------------------------------------------------------------------------------
> >
> > Trying to get: NM_019072
> >
> > org.biojava.bio.BioException: Failed to read Genbank sequence
> >
> > at
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(
> > GenbankRichSequenceDB.java:157)
> >
> > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java
> :162)
> >
> > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146)
> >
> > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195)
> >
> > 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)
> >
> > ... 3 more
> >
> > Caused by: java.lang.IllegalArgumentException: Could not find
> constructor
> > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class
> > java.lang.String,null)
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:78)
> >
> > at org.biojavax.RichObjectFactory.getObject(
> RichObjectFactory.java
> > :104)
> >
> > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(
> > GenbankFormat.java:387)
> >
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >
> > ... 4 more
> >
> > Caused by: java.lang.NullPointerException
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:59)
> >
> > ... 7 more
> >
> >
> --------------------------------------------------------------------------------
> >
> > Trying to get: NM_017884
> >
> > org.biojava.bio.BioException: Failed to read Genbank sequence
> >
> > at
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(
> > GenbankRichSequenceDB.java:157)
> >
> > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java
> :162)
> >
> > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146)
> >
> > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195)
> >
> > 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)
> >
> > ... 3 more
> >
> > Caused by: java.lang.IllegalArgumentException: Could not find
> constructor
> > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class
> > java.lang.String,null)
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:78)
> >
> > at org.biojavax.RichObjectFactory.getObject(
> RichObjectFactory.java
> > :104)
> >
> > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(
> > GenbankFormat.java:387)
> >
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >
> > ... 4 more
> >
> > Caused by: java.lang.NullPointerException
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:59)
> >
> > ... 7 more
> >
> >
> --------------------------------------------------------------------------------
> >
> > Trying to get: NM_022107
> >
> > org.biojava.bio.BioException: Failed to read Genbank sequence
> >
> > at
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(
> > GenbankRichSequenceDB.java:157)
> >
> > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java
> :162)
> >
> > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146)
> >
> > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195)
> >
> > 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)
> >
> > ... 3 more
> >
> > Caused by: java.lang.IllegalArgumentException: Could not find
> constructor
> > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class
> > java.lang.String,null)
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:78)
> >
> > at org.biojavax.RichObjectFactory.getObject(
> RichObjectFactory.java
> > :104)
> >
> > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(
> > GenbankFormat.java:387)
> >
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >
> > ... 4 more
> >
> > Caused by: java.lang.NullPointerException
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:59)
> >
> > ... 7 more
> >
> >
> ---------------------------------------------------------------------------------
> >
> > Trying to get: NM_031418
> >
> > org.biojava.bio.BioException: Failed to read Genbank sequence
> >
> > at
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(
> > GenbankRichSequenceDB.java:157)
> >
> > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java
> :162)
> >
> > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146)
> >
> > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195)
> >
> > 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)
> >
> > ... 3 more
> >
> > Caused by: java.lang.IllegalArgumentException: Could not find
> constructor
> > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class
> > java.lang.String,null)
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:78)
> >
> > at org.biojavax.RichObjectFactory.getObject(
> RichObjectFactory.java
> > :104)
> >
> > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(
> > GenbankFormat.java:387)
> >
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >
> > ... 4 more
> >
> > Caused by: java.lang.NullPointerException
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:59)
> >
> > ... 7 more
> >
> >
> ---------------------------------------------------------------------------------------
> >
> > Trying to get: NM_030809
> >
> > org.biojava.bio.BioException: Failed to read Genbank sequence
> >
> > at
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(
> > GenbankRichSequenceDB.java:157)
> >
> > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java
> :162)
> >
> > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146)
> >
> > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195)
> >
> > 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)
> >
> > ... 3 more
> >
> > Caused by: java.lang.IllegalArgumentException: Could not find
> constructor
> > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class
> > java.lang.String,null)
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:78)
> >
> > at org.biojavax.RichObjectFactory.getObject(
> RichObjectFactory.java
> > :104)
> >
> > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(
> > GenbankFormat.java:387)
> >
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >
> > ... 4 more
> >
> > Caused by: java.lang.NullPointerException
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:59)
> >
> > ... 7 more
> >
> >
> -------------------------------------------------------------------------------------
> >
> > Trying to get: NM_032731
> >
> > org.biojava.bio.BioException: Failed to read Genbank sequence
> >
> > at
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(
> > GenbankRichSequenceDB.java:157)
> >
> > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java
> :162)
> >
> > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146)
> >
> > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195)
> >
> > 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)
> >
> > ... 3 more
> >
> > Caused by: java.lang.IllegalArgumentException: Could not find
> constructor
> > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class
> > java.lang.String,null)
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:78)
> >
> > at org.biojavax.RichObjectFactory.getObject(
> RichObjectFactory.java
> > :104)
> >
> > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(
> > GenbankFormat.java:387)
> >
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >
> > ... 4 more
> >
> > Caused by: java.lang.NullPointerException
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:59)
> >
> > ... 7 more
> >
> >
> ------------------------------------------------------------------------------------
> >
> > Trying to get: NM_001029888
> >
> > org.biojava.bio.BioException: Failed to read Genbank sequence
> >
> > at
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(
> > GenbankRichSequenceDB.java:157)
> >
> > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java
> :162)
> >
> > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146)
> >
> > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195)
> >
> > 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)
> >
> > ... 3 more
> >
> > Caused by: java.lang.IllegalArgumentException: Could not find
> constructor
> > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class
> > java.lang.String,null)
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:78)
> >
> > at org.biojavax.RichObjectFactory.getObject(
> RichObjectFactory.java
> > :104)
> >
> > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(
> > GenbankFormat.java:387)
> >
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >
> > ... 4 more
> >
> > Caused by: java.lang.NullPointerException
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:59)
> >
> > ... 7 more
> >
> >
> ------------------------------------------------------------------------------------
> >
> > Trying to get: NM_001029869
> >
> > org.biojava.bio.BioException: Failed to read Genbank sequence
> >
> > at
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(
> > GenbankRichSequenceDB.java:157)
> >
> > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java
> :162)
> >
> > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146)
> >
> > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195)
> >
> > 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)
> >
> > ... 3 more
> >
> > Caused by: java.lang.IllegalArgumentException: Could not find
> constructor
> > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class
> > java.lang.String,null)
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:78)
> >
> > at org.biojavax.RichObjectFactory.getObject(
> RichObjectFactory.java
> > :104)
> >
> > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(
> > GenbankFormat.java:387)
> >
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >
> > ... 4 more
> >
> > Caused by: java.lang.NullPointerException
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:59)
> >
> > ... 7 more
> >
> >
> ------------------------------------------------------------------------------------
> >
> > Trying to get: NM_182572
> >
> > org.biojava.bio.BioException: Failed to read Genbank sequence
> >
> > at
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(
> > GenbankRichSequenceDB.java:157)
> >
> > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java
> :162)
> >
> > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146)
> >
> > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195)
> >
> > 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)
> >
> > ... 3 more
> >
> > Caused by: java.lang.IllegalArgumentException: Could not find
> constructor
> > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class
> > java.lang.String,null)
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:78)
> >
> > at org.biojavax.RichObjectFactory.getObject(
> RichObjectFactory.java
> > :104)
> >
> > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(
> > GenbankFormat.java:387)
> >
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> > RichStreamReader.java:109)
> >
> > ... 4 more
> >
> > Caused by: java.lang.NullPointerException
> >
> > at org.biojavax.SimpleRichObjectBuilder.buildObject(
> > SimpleRichObjectBuilder.java:59)
> >
> > ... 7 more
> >
> >
> >
> >
> >
>
>
--
Best Regards,
Seth Johnson
Senior Bioinformatics Associate
Ph: (202) 470-0900
Fx: (775) 251-0358
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