[BioPython] BLAST XML parser trouble

[B. Brazelton]

I put in 'tblastx 2.2.15 [Oct-15-2006]' and it worked fine.

Thanks for your help, sorry for the newbie question.

(FYI, I was using results generated from the CAMERA database
(http://camera.calit2.net/), and I was using the main biopython
tutorial and cookbook from biopython.org. thanks again,

BB

On 10/8/07, Michiel De Hoon <mdehoon at c2b2.columbia.edu> wrote:
> How did you produce the XML file? In particular, which Blast version did you
> use?
> The Blast XML parser trips over the following line in your XML file:
>
>     <BlastOutput_version>unspecified</BlastOutput_version>
>
> This is supposed to be:
>
>   <BlastOutput_version>BLASTP 2.2.12 [Aug-07-2005]</BlastOutput_version>
>
> , of course depending on which Blast version you are using.
>
> --Michiel
>
>
>
> Michiel de Hoon
> Center for Computational Biology and Bioinformatics
> Columbia University
> 1150 St Nicholas Avenue
> New York, NY 10032
>
>
>
> -----Original Message-----
> From: biopython-bounces at lists.open-bio.org on behalf of B. Brazelton
> Sent: Mon 10/8/2007 8:33 PM
> To: biopython at biopython.org
> Subject: [BioPython] BLAST XML parser trouble
>
> I tried to follow the BLAST XML parser example in the tutorial, but I
> always get the following error when attempting to iterate through the
> records:
>
> Traceback (most recent call last):
>   File "BlastXML_Parser.py", line 10, in ?
>     for blast_record in blast_records:
>   File
> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site-
> packages/Bio/Blast/NCBIXML.py",
> line 572, in parse
>     expat_parser.Parse(text, False)
>   File
> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site-
> packages/Bio/Blast/NCBIXML.py",
> line 98, in endElement
>     eval("self.%s()" % method)
>   File "<string>", line 0, in ?
>   File
> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site-
> packages/Bio/Blast/NCBIXML.py",
> line 215, in _end_BlastOutput_version
>     self._header.version = self._value.split()[1]
> IndexError: list index out of range
>
> All I did was:
>
> result_handle = open('NifH_Blast.xml')
> from Bio.Blast import NCBIXML
> blast_records = NCBIXML.parse(result_handle)
> for blast_record in blast_records:
>     ... etc
>
> I put my script and xml file here:
> http://www.staff.washington.edu/braz/files
>
> I'm using biopython 1.43, and I get the same error on both Python
> 2.3.5 and Python 5.
>
> It seems like my commands are exactly what is in the tutorial, so I'm
> confused. My best guess is that there is a difference in the XML
> format, but it's NCBI XML. Thanks for any help,
>
> Bill Brazelton
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