[BioPython] Problems runing BLAST

[Bruno Santos]

I wasn't using any XML file as intermediate, I was parsing the blast results
directly. But it was really a problem with the databases. Now it's solved.

My question now is another one, I'm blasting a multifasta file, so I need to
know which results belongs to which query sequence ID. I Know I can simply
assume that the blast result is ordered according to the sequences in the
fasta file, but is any other away to obtain the query ID directly using the
Blast Record class?

Thanks in advance,
Bruno Santos

-----Mensagem original-----
De: p.j.a.cock at googlemail.com [mailto:p.j.a.cock at googlemail.com] Em nome de
Peter
Enviada: quarta-feira, 23 de Janeiro de 2008 21:07
Para: Sebastian Bassi
Cc: Bruno Santos; biopython at biopython.org
Assunto: Re: [BioPython] Problems runing BLAST

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