[Biopython] qBlast Error and Entrez module

[Peter]

On Mon, Aug 10, 2009 at 4:10 PM, Peter<biopython at maubp.freeserve.co.uk> wrote:
> On Mon, Aug 10, 2009 at 3:31 PM, Rodrigo
> faccioli<rodrigo_faccioli at uol.com.br> wrote:
>> Hello,
>>
>> I've tried to execute a blast from NCBI. In this way, I'm using the NCBI
>> module from Biopython. I read the Biopython Tutorial its Chapter 7. So, my
>> code is below.
>>
>>        result_handle = NCBIWWW.qblast("blastn", "nr",
>> "TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN")
>>        blast_results = result_handle.read()
>>        save_file = open( "1CRN_Blast.xml", "w")
>>        save_file.write(blast_results)
>>        save_file.close()
>>
>> However, when I execute this code, I receive the error message: raise
>> ValueError("No RID and no RTOE found in the 'please wait' page."
>>
>> I don't know what I'm doing wrong. So, if somebody can help me, I thank.
>
> I don't see anything wrong with that line, but it isn't working for me either.
> Odd. Perhaps the NCBI have changed something... I'll get back to you.

It is actually a simple problem: You are using a protein query but BLASTN
requires a nucleotide sequence. The NCBI does actually try and tell us
this, but Biopython doesn't (currently) know how to extract the error
message to show you.

Peter