[BioPython] Problems runing BLAST
Peter
biopython at maubp.freeserve.co.uk
Wed Jan 23 21:07:07 UTC 2008
On 1/23/08, Sebastian Bassi <sbassi at gmail.com> wrote:
> On Jan 23, 2008 3:55 PM, Bruno Santos <bsantos at biocant.pt> wrote:
> > raise SyntaxError("Your XML file did not start <?xml...")
> > SyntaxError: Your XML file did not start <?xml...
>
> Can you show us the result of:
> head your_xml_file.xml
Seeing the start of the XML file would be very helpful. And if is
empty, what has been written to the error handle? I would guess maybe
the database is in a new location or something simple like that...
print error_info.read()
Another thing to check is the version of Biopython on the new machine.
Earlier versions would default to asking blast for plain text output
instead of XML.
Peter
More information about the Biopython
mailing list