[Biojava-l] Parsing Genbank-sequences from NCBI
Seth Johnson
johnson.biotech at gmail.com
Tue Aug 8 15:44:42 UTC 2006
Hello,
Works perfect now!!! Thanks for looking into it.
On 8/8/06, Richard Holland <holland at ebi.ac.uk> wrote:
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hello all.
>
> Sorry for the delay - I was off sick yesterday.
>
> The bug had been fixed in the BioSQL side of things, but not when merely
> loading sequences into memory without persisting them to the database.
> I've been through and checked and hopefully fixed this now in CVS. Let
> me know how you get on!
>
> cheers,
> Richard
>
>
> David Scott wrote:
> > 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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>
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>
--
Best Regards,
Seth Johnson
Senior Bioinformatics Associate
Ph: (202) 470-0900
Fx: (775) 251-0358
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