[Biojava-l] Parsing Genbank-sequences from NCBI

David Scott david at autohandle.com
Sat Aug 5 22:55:23 UTC 2006


hi seth-

nm_006145 loaded for me and i recreated the genbank entry with only 
minor differences - now, i'm at a loss - maybe we should wait for the 
other guys to get online after the weekend - they are much better at 
this remote debugging than i am.

sorry i just couldn't help-
david

Seth Johnson wrote:
> 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 
> <mailto: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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