[Biojava-l] Question about BioJava DASClient classes

Patrick McConnell MCCon012@mc.duke.edu
Wed, 11 Sep 2002 16:09:17 -0400

You are right.  I upgraded to 3.3 and it works fine.  Thanks : - )

Incidentally, it breaks on fasta34t10d3 - the error is:

org.biojava.utils.ParserException: Fasta parser failed to recognise line type
Parsing line: 37
; pg_open-ext: -10 -2


Keith James <kdj@sanger.ac.uk> on 09/11/2002 01:36:59 PM

To:    "Patrick McConnell" <MCCon012@mc.duke.edu>
cc:    biojava-l@biojava.org

Subject:    Re: [Biojava-l] Question about BioJava DASClient classes

>>>>> "Patrick" == Patrick McConnell <MCCon012@mc.duke.edu> writes:

    Patrick> I am getting a NullPointerException running Fasta2XML in
    Patrick> demos/eventbasedparsing on a test fasta run using -m 10
    Patrick> output.  I have pasted the output/stack trace at the end.

    Patrick> Any ideas?

Hi Patrick,

Looking at the output my guess is that you are using quite an old
version of Fasta and that the m10 format has changed. The parser was
written and tested against version 3.3t08.

I've just had a look at some output from a slightly older version than
yours (version 2.0u4 Feb., 1996) and noticed what may be a
show-stopper. It doesn't terminate each search output with >>><<<. The
parser relies heavily on this because a BlastLikeDataSetCollection may
contain many searches and this token is the search delimiter.

Firstly, I'll update the Javadoc to specify the version supported.

Secondly, if your output does have a terminal >>><<< then I can
probably fix the parser to accept it if you can send me a
copy. Otherwise the only alternative is to use a more recent version
of Fasta.



- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -