[Biojava-l] Problem Solved Re: problem with CookBook:Blast:Parser

[Ozgur Ozturk]

Hi,
      Another code in demos ( BioJava/biojava-1.5/demos/blastxml ) could
handle my xml file.
I guess the problem is solved. Thanks.
(But if the BlastParser code from the
cookbook<http://www.biojava.org/wiki/BioJava:CookBook:Blast:Parser>is
deprecated, you may want to update it.)

Best regards,
Ozgur (Oscar) Ozturk,
http://www.cse.ohio-state.edu/~ozturk/
Mobile Phone: (614) 805-4370

On 10/23/07, Ozgur Ozturk <ozgur7 at gmail.com> wrote:
>
> Hi,
>    I am receiving the following error when I use BlastParser code from the
> cookbook <http://www.biojava.org/wiki/BioJava:CookBook:Blast:Parser> :
>
> org.xml.sax.SAXException: Could not recognise the format of this file as
> one supported by the framework.
>     at org.biojava.bio.program.sax.BlastLikeSAXParser.parse(
> BlastLikeSAXParser.java:182)
>     at org.arabidopsis.test.BlastParser.main(BlastParser.java:44)
>
> I have generated the xml file using this command:
> blast-2.2.17/bin/blastall -p blastp -d brAll -i tester -b 300 -m 7 >
> tempresult.xml
>
> Then pass it to BlastParser:
> BlastParser tempresult.xml
>
> Thanks for your help in advance,
> --
> Best regards,
> Ozgur (Oscar) Ozturk,
> http://www.cse.ohio-state.edu/~ozturk/<http://www.cse.ohio-state.edu/%7Eozturk/>
> Mobile Phone: (614) 805-4370