[BioPython] XML Parser problem

[Michiel Jan Laurens de Hoon]

It looks like you are running an old version of Blast. When blasting 
several sequences at the same time, old blast makes an output file 
consisting of several XML files concatenated together. According to the 
XML specification, this is not a well-formed XML file.

There are two things you can do:
1) Continue using the old blast, and use NCBIStandalone.Iterator to 
parse the output file. See section 3.1.6 in the tutorial.
2) Update to the new blast, which creates a well-formed XML file, and 
see my next mail about the XML parser.

--Michiel.


alper soyler wrote:
> Dear all,
> 
> I run blastall with option -m7 to save the resulting file as xml. However, when I open the xml file with firefox, it gave the following error message.
> 
> XML Parsing Error: junk after document element
> Location: file:///home/alper/Desktop/genes/combinedblastfile.xml
> Line Number 38, Column 1:
> <?xml version="1.0"?>
> ^


-- 
Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1130 St Nicholas Avenue
New York, NY 10032