[Biojava-l] Parsing Genbank-sequences from NCBI
David Scott
david at autohandle.com
Fri Aug 4 20:52:47 UTC 2006
hi seth-
you are right - the fix for null titles was put in
BioSQLRichObjectBuilder on 7.19 - i guess there must be a bug in the fix
- i offered to check the fix - so i'll have to hang my head in shame.
i'm looking at the code now - not the 1st time for me and i don't see
the problem. i'll try one of your test cases - but i can't get to it
until tomorrow.
don't tell anyone i messed up-
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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