[Biojava-l] Parsing Genbank-sequences from NCBI
Seth Johnson
johnson.biotech at gmail.com
Fri Aug 4 15:59:56 UTC 2006
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
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