[Biojava-dev] NullPointerException from BlastSAXParser.java

Sun Oct 9 21:34:08 EDT 2005

I would like to reiterate this.

The BLAST text output has never been consistent between versions. Seems 
NCBI has problems with backwards compatability too : ) This has made it 
difficult to maintain the parsers.

The XML version is much safer. Although for a while it didn't follow it's 
own DTD it seems that now it does and has done for a while.

- Mark

"W. Eric Trull" <wetrull at yahoo.com>
Sent by: biojava-dev-bounces at portal.open-bio.org
10/08/2005 02:45 AM

        To:     biojava-dev at biojava.org
        cc:     Mark Schreiber/GP/Novartis at PH
        Subject:        RE: [Biojava-dev] NullPointerException from BlastSAXParser.java

I'll switch to the XML output and parser...seems more sane anyway.

Thanks!

-Eric Trull

--- "Sicotte, Hugues (NIH/NCI)" <sicotteh at mail.nih.gov> wrote:

> I've been through this before when I was working for
> NCBI.
> 
> The answer was that the text output of BLAST was never a supported 
format.
> The only supported format is the XML Blast Output.
> http://ccgb.umn.edu/~crow/projects/xmlblast/example.html
> 
> also
> 
> In the case of parsing multiple blast files,
> breaking on "Searching..." is not a good idea
> because if the parameters are wrong or the query sequence
> too low complexity, this String is not emitted by the program.
> 
> 
> Hugues Sicotte
> 
> 
> -----Original Message-----
> From: W. Eric Trull [mailto:wetrull at yahoo.com]
> Sent: Friday, October 07, 2005 12:05 PM
> To: biojava-dev at biojava.org
> Cc: mark.schreiber at novartis.com
> Subject: Re: [Biojava-dev] NullPointerException from BlastSAXParser.java
> 
> 
> Should I raise this as an issue with NCBI?  Seems like it makes writting
> parsing routines more difficult.
> 
> Thanks.
> 
> -Eric Trull
> 
> --- mark.schreiber at novartis.com wrote:
> 
> > Looks like there might be a difference in the Windows output. I will 
try 
> > to take a look at this over the next few days. Probably need to change
> the
> 
> > BlastSAXParser to look for something other than Searching so that this 

> > will get parsed as well.
> > 
> > - Mark
> > 
> > 
> > 
> > 
> > 
> > "W. Eric Trull" <wetrull at yahoo.com>
> > 10/06/2005 11:01 PM
> > 
> > 
> >         To:     biojava-dev at biojava.org
> >         cc:     Mark Schreiber/GP/Novartis at PH
> >         Subject:        Re: [Biojava-dev] NullPointerException from
> > BlastSAXParser.java
> > 
> > 
> > Hello Mark,
> > 
> > Here is what I've done, using NCBI Blast 2.0.11, Windows XP, JDK 1.4.2
> > 
> > 1.  Downloaded the PDB's pdb_seqres.txt
> > 2.  Created a blast database (after changing the deflines):
> >         C:\blast-2.0.11\formatdb.exe
> >             -t "PDB" 
> >             -i blast\pdb_seqres.txt
> >             -l blast\pdb_formatdb.log
> >             -o T
> >             -n blast\pdb
> > 3.  BLASTed 26SPS9_Hs:
> >         C:\blast-2.0.11\blastall.exe
> >             -p blastp
> >             -d blast\pdb
> >             -i 26SPS9_Hs.fasta
> >             -o 26SPS9_Hs.blast
> > 4.  Tried to parse 26SPS9_Hs.blast using the class shown in BioJava in 

> > Anger
> > and BlastEcho, both of which give me the NullPointerException.  The 
> > beginning
> > of 26SPS9_Hs.blast file is shown below, the entire file is attached. 
> > 
> > Please let me know if you see anything obviously wrong with the way 
I'm 
> > doing
> > the BLAST.  I'm going to cvs checkout the BioJava source code and have 
a 
> > look
> > at the JUnit test later today.
> > 
> > Thanks!
> > 
> > -Eric Trull
> > 
> > -------- 26SPS9_Hs.blast --------
> > BLASTP 2.0.11 [Jan-20-2000]
> > 
> > 
> > Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. 
Schaffer,
> 
> > Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
> > "Gapped BLAST and PSI-BLAST: a new generation of protein database 
search
> > programs",  Nucleic Acids Res. 25:3389-3402.
> > 
> > Query= 26SPS9_Hs 
> >          (176 letters)
> > 
> > Database: PDB
> >            78,094 sequences; 17,596,117 total letters
> > 
> > 
> > 
> > Score 
> 
> > E
> > Sequences producing significant alignments: (bits)
> 
> > Value
> > 
> > pdb|1UFM|A Cop9 Complex Subunit 4 39
> 
> > 0.003
> > .
> > .
> > .
> > -------- 26SPS9_Hs.blast --------
> > 
> > 
> > --- mark.schreiber at novartis.com wrote:
> > 
> > > Hello -
> > > 
> > > This is very odd.
> > > 
> > > The JUnit tests currently pass using the files in 
> > > /tests/files/org/biojava/bio/programs/ssbind  These BLAST files all
> have
> 
> > 
> > > the string "Searching....". Maybe there is a variation in the 
windows 
> > > output?
> > > 
> > > Can you post at least the header of your output to the list 
(preferably
> 
> > an 
> > > entire example output)?
> > > 
> > > - Mark
> > > 
> > > 
> > > 
> > > 
> > > 
> > > "W. Eric Trull" <wetrull at yahoo.com>
> > > Sent by: biojava-dev-bounces at portal.open-bio.org
> > > 10/06/2005 06:11 AM
> > > 
> > > 
> > >         To:     biojava-dev at biojava.org
> > >         cc:     (bcc: Mark Schreiber/GP/Novartis)
> > >         Subject:        [Biojava-dev] NullPointerException from
> > > BlastSAXParser.java
> > > 
> > > 
> > > Hello all,
> > > 
> > > I'm new to the list, but have done as much archive searching, Google
> > > searching, and debugging as I can on the problem I describe here.
> > > 
> > > I'm trying to parse NCBI BLAST output (as shown in BioJava in 
Anger), 
> > but
> > > keep getting a NullPointerException.  One of my searches turned up
> using
> > > BlastEcho to debug the problem, but that also throws the
> > > NullPointerException:
> > > 
> > > startSearch
> > >                  SearchProp:             program: ncbi-blastp
> > >                  SearchProp:             version: 2.0.11
> > > java.lang.NullPointerException
> > >                  at
> > >
> >
>
org.biojava.bio.program.sax.BlastSAXParser.interpret(BlastSAXParser.java:215
> )
> > >                  at 
> > > 
> > 
org.biojava.bio.program.sax.BlastSAXParser.parse(BlastSAXParser.java:164)
> > >                  at
> > >
> >
>
org.biojava.bio.program.sax.BlastLikeSAXParser.onNewDataSet(BlastLikeSAXPars
> er.java:311)
> > >                  at
> > >
> >
>
org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.
> java:274)
> > >                  at
> > >
> >
>
org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java
> :160)
> 
=== message truncated ===

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